Compositions and methods that promote hypoxia or the hypoxia response for treatment and prevention of mitochondrial dysfunction and oxidative stress disorders

ABSTRACT

Methods of promoting hypoxia or the hypoxia response for the treatment or prevention of mitochondrial dysfunction and oxidative stress disorders are described. Methods for screening for targets of mitochondrial dysfunction and oxidative stress disorders are also described.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/204,285 filed Aug. 12, 2015 and U.S. Provisional Application No.62/268,213 filed Dec. 16, 2015, the contents of both of which areincorporated herein by reference in their entireties.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under Grant No.DE-FG02-97ER25308 awarded by the Department of Energy. The Governmenthas certain rights in this invention.

TECHNICAL FIELD

The present invention relates generally to compositions and methods thatpromote hypoxia or the hypoxia response for treating or preventingmitochondrial dysfunction and oxidative stress disorders.

BACKGROUND

There is growing evidence that mitochondrial dysfunction is associatedwith a broad range of human diseases. Virtually all common,age-associated disorders, including type 2 diabetes, neurodegeneration,and sarcopenia, are accompanied with a quantitative decline in theactivity of the mitochondrial respiratory chain (Vafai et al., Nature,491:374-83 (2012); Parikh et al., Curr Treat Options Neurol. 11:414-30(2009). Monogenic disorders of the mitochondrial respiratory chainrepresent the largest class of inborn errors of metabolism. To date,lesions in over 150 genes, encoded by the nuclear or mitochondrial(mtDNA) genome, have been identified as disease-causing. Mutations inthese genes lead to a biochemical deficiency of one or more of therespiratory chain complexes, leading to either tissue-specific ormultisystemic disease. Management of these disorders remains incrediblychallenging, owing to the remarkable genetic heterogeneity andpleiotropy. Current treatments are limited to ad hoc administration ofvitamins and co-factors, none of which have proven efficacy. A moregeneral and effective therapeutic is needed for the treatment ofmitochondrial dysfunction.

A major challenge in targeting mitochondrial disease lies in the factthat the organelle plays diverse roles in cellular metabolism.Classically, mitochondrial disease pathology is thought to arise from anenergy supply-demand imbalance. However, redox state, nucleotidebiosynthesis, ROS homeostasis, regulation of apoptosis, calciumsignaling and fatty acid oxidation may be impaired in disease states. Itis notable that mitochondrial disorders can be highly tissue-specific,and episodic (Haas et al., Pediatrics. 120, 1326-33 (2007)). Individualswith identical genetic lesions can follow completely distinct clinicaltrajectories. Such observations suggest that existing cellular pathwaysmay buffer against lesions in unaffected tissues.

SUMMARY

A genome-wide clustered regularly interspaced short palindrome repeats(CRISPR) screen was performed to spotlight endogenous pathways thatbuffer against mitochondrial respiratory chain dysfunction. The screenidentified Von Hippel Landau (VHL)-inhibition and thus the hypoxiaresponse, as a suppressor of mitochondrial disease. It was shown thatgenetic or small molecule activation of the hypoxia inducibletranscription factors (HIF) rescued cellular growth defects caused byrespiratory chain deficiency. The small molecule FG-4592 rescued thedisease state in a variety of cell types and at multiple steps(complexes I, III, V) of the electron transport chain, demonstrating thebroad applicability of this therapeutic approach as described herein.FG-4592 treatment rewired energy metabolism, including an increase inthe glycolytic capacity of cells, as well as a suppression of basalrespiration. FG-4592 treatment in vivo alleviated the sensitivity ofzebrafish embryos to mitochondrial dysfunction. These findingsdemonstrated that bypassing cellular oxygen sensing to trigger the HIFresponse was protective during states of respiratory chain inhibition.In an in vivo mouse model of mitochondrial disease, hypoxic breathing(11% O₂) was surprisingly found to be protective in diseased animalswhereas mild hyperoxia (55% O₂ breathing) was toxic. The mouse model ofmitochondrial disease evaluated herein is characterized by excessoxidative stress, indicating that reducing oxygen availability (and thusthe availability of oxygen needed to produce reactive oxygen species) isan effective means to treat disorders characterized by excess oxidativestress. These findings indicate that promoting hypoxia or the hypoxiaresponse can be used to treat or prevent mitochondrial dysfunction andoxidative stress disorders. In addition, hypoxia was found to protectagainst inflammation-induced death in the mouse model of mitochondrialdisease, indicating that promoting hypoxia or the hypoxia response canbe used to treat or prevent inflammatory disorders.

In one aspect, the disclosure provides a method of treating orpreventing mitochondrial dysfunction, an oxidative stress disorder, oran inflammatory disorder in a subject in need thereof comprisingincreasing the activity of a hypoxia response in the subject. Increasingthe activity of a hypoxia response can be achieved by, for example,exposing the subject to hypoxia. In some embodiments, the hypoxiaresponse may include, but is not limited to, one or more of thefollowing: a physiological response or a trigger of a hypoxia response.

In another aspect, the disclosure provides a method of treating orpreventing mitochondrial dysfunction, an oxidative stress disorder, oran inflammatory disorder in a subject in need thereof, the methodcomprising administering to the subject by inhalation a therapeuticallyeffective amount of a therapeutic gas at normobaria comprising between 5to 20% O₂. In some embodiments, the therapeutic gas comprises between 10to 15% O₂, between 10 to 12% O₂, or about 11% O₂.

In another aspect, the disclosure provides a method of treating orpreventing mitochondrial dysfunction, an oxidative stress disorder, oran inflammatory disorder in a subject in need thereof, the methodcomprising causing the subject to breathe a therapeutically effectiveamount of air in a hypobaric chamber. In some embodiments, the hypobaricchamber has an atmospheric pressure equal to the atmospheric pressure atan elevation between 1,500 to 10,000 meters above sea level (e.g., anatmospheric pressure equal to the atmospheric pressure at an elevationbetween 1,500 to 8,000 meters or between 2,000 to 4,500 meters above sealevel).

In another aspect, the disclosure provides a method of increasing theactivity of a hypoxia response in a subject in need thereof comprisingincreasing the stability or the activation of HIF proteins in thesubject.

In another aspect, the disclosure provides a treating or preventingmitochondrial dysfunction, an oxidative stress disorder, or aninflammatory disorder in a subject in need thereof comprising increasingcellular glycolysis in the subject.

In another aspect, the disclosure provides a method of treating orpreventing mitochondrial dysfunction, an oxidative stress disorder, oran inflammatory disorder in a subject in need thereof comprisingsuppressing cellular basal respiration in the subject.

In some embodiments, nitric oxide is administered in combination with amethod described herein. In some embodiments, the therapeutic gascomprises nitric oxide (e.g., wherein the concentration of nitric oxidein the therapeutic gas is at least 5 ppm, at least 10 ppm, at least 20ppm, or is in the range of 0.5 ppm to 80 ppm).

In some embodiments, xenon is administered in combination with a methoddescribed herein. In some embodiments, the therapeutic gas comprisesxenon (e.g., wherein the therapeutic gas comprises between 20-70%xenon).

In some embodiments, an agent that reduces pulmonary hypertension orraises the cGMP level in other cells (e.g., a phosphodiesteraseinhibitor or a soluble guanylate cyclase sensitizer) is administeredeither systemically or by inhalation to the lung in combination with amethod described herein.

Examples of phosphodiesterase inhibitors include: Zaprinast® (M&B 22948;2-o-propoxyphenyl-8-azapurine-6-one; Rhone-Poulenc Rorer, DagenhamEssex, UK); WIN 58237(1-cyclopentyl-3-methyl-6-(4-pyridyl)pyrazolo[3,4-d]pyrimidin-4-(5H)-one;Silver et al. (1994) J. Pharmacol. Exp. Ther. 271:1143); SCH 48936((+)-6a,7,8,9,9a,10,11,11a-octahydro-2,5-dimethyl-3H-pentalen(6a,1,4,5)imidazo[2,1-b]purin-4(5H)-one; Chatterjee et al. (1994) Circulation90:1627, abstract no. 3375); KT2-734(2-phenyl-8-ethoxycycloheptimidazole; Satake et al. (1994) Eur. J.Pharmacol. 251:1); E4021 (sodium1-[6-chloro-4-(3,4-methylenedioxybenzyl)-aminoquinazolin-2-y]piperidine-4-carboxylatesesquihydrate; Saeki et al. (1995) J. Pharmacol. Exp. Ther. 272:825);sildenafil (Viagra®); tadalafil (Cialis®); and vardenafil (Levitra®).

Examples of compounds that sensitize soluble guanylate cyclase include:3-(5′-hydroxymethyl-2′-furyl)-1-benzylindazole (“YC-1”; Russwurm (2002)J. Biol. Chem. 277:24883; Schmidt et al. (2001) Mol. Pharmacol. 59:220;and Friebe et al. (1998) Mol. Pharmacol. 54:962); compounds looselybased on YC-1 such as the pyrazolopyridine BAY 41-2272 (Stasch et al.(2001) Nature 410:212), the BAY 41-2272 derivatives ortho-(BAY 50-6038),meta-(BAY 51-9491) and para-PAL-(BAY 50-8364) (Becker et al. (2001) BMCPharmacol. 1:13), and BAY 41-8543 (Stasch et al. (2002) Brit. J.Pharmacol. 135:333);2-[1-(2-fluorobenzyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(4-morpholinyl)-4,6-pyrimidine-diamine;2-[1-(2-fluorobenzyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-(4-pyridinyl)-4-pyrimidmamine;methyl-4,6-diamino-2-[1-(2-fluorobenzyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-pyrimidinyl-(methyl)carbamate;methyl-4,6-diamino-2-[1-(2-fluorobenzyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-5-pyrimidinyl-carbamate;and4-[((4-carboxybutyl)-{2-[(4-phenethylbenzyl)oxy]phenethyl}amino)methyl]benzoicacid.

In some embodiments, the therapeutic gas is administered to the subjectcontinuously (e.g., for at least three minutes, at least 15 minutes, atleast one hour, at least eight hours, or at least 24 hours). In someembodiments, the therapeutic gas is administered to the subjectintermittently.

In some embodiments, the therapeutic gas is humidified and administeredto the subject by nasal prongs, a face mask, an enclosed tent orchamber, an intra-tracheal catheter, an endotracheal tube, or atracheostomy tube. For example, the therapeutic gas can be administeredto the subject by a tent that is positioned over a bed or a crib onwhich the subject is placed.

In some embodiments, arterial oxygen saturation (SpO₂) is measured inthe subject one or more times after administration of the therapeuticgas to the subject (e.g., continuously during administration of thetherapeutic gas to the subject); and/or arterial partial oxygen pressure(PaO₂) is measured in the subject one or more times after administrationof the therapeutic gas to the subject (e.g., continuously duringadministration of the therapeutic gas to the subject). In someembodiments, the measured SpO₂ value is used to feedback andautomatically determine the concentration of inspired oxygen so as tomaintain SpO₂ in the subject in the range of 50-90%; and/or the measuredPaO₂ value is used to feedback and automatically determine theconcentration of inspired oxygen so as to maintain PaO₂ in the subjectin the range of 25 mm Hg to 70 mm Hg.

In any of the methods described herein, the subject optionally has amitochondrial disorder. The mitochondrial disorder is in some examples amonogenic mitochondrial disorder.

In some examples, the mitochondrial disorder is characterized by amutation in a gene selected from the group consisting of AARS2, AASS,ABAT, ABCB6, ABCB7, ABCD1, ACACA, ACAD8, ACAD9, ACADM, ACADS, ACADSB,ACADVL, ACAT1, ACO2, ACSF3, ACSL4, ADCK3, ADCK4, AFG3L2, AGK, AGXT,AIFM1, AK2, ALAS2, ALDH18A1, ALDH2, ALDH3A2, ALDH4A1, ALDH5A1, ALDH6A1,ALDH7A1, AMACR, AMT, APOPT1, ATIC, ATP5A1, ATPSE, ATP6, ATP8, ATPAF2,ATXN2, AUH, BAX, BCKDHA, BCKDHB, BCKDK, BCS1L, BOLA3, C10orf2, C12orf65,CASA, CARS2, CASP8, CAT, CEP89, CHCHD10, CISD2, CLPB, CLPP, COA5, COA6,COASY, COQ2, COQ4, COQ6, COQ9, COX1, COX10, COX14, COX15, COX2, COX20,COX3, COX4I2, COX6A1, COX6B1, COX7B, CPDX, CPS1, CPT1A, CPT2, CYBSA,CYB5R3, CYC1, CYCS, CYP11A1, CYP11B2, CYP24A1, CYP27A1, CYP27B1, CYTB,D2HGDH, DARS2, DBT, DGUOK, DHCR24, DHODH, DHTKD1, DIABLO, DLAT, DLD,DMGDH, DMPK, DNA2, DNAJC19, DNM1L, EARS2, ECHS1, ELAC2, ETFA, ETFB,ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FECH, FH, FKBP10, FOXRED1, FXN,GARS, GATM, GCDH, GCSH, GDAP1, GFER, GFM1, GK, GLDC, GLRX5, GLUD1,GLYCTK, GPI, GPX1, GRHPR, GTPBP3, HADH, HADHA, HADHB, HARS2, HCCS,HIBCH, HK1, HMBS, HMGCL, HMGCS2, HOGA1, HSD17B10, HSD17B4, HSPD1, HTRA2,IDH2, IDH3B, ISCA2, ISCU, IVD, KARS, KIF1B, KRT5, L2HGDH, LARS2, LIAS,LONP1, LRPPRC, LYRM4, LYRM7, MAOA, MARS2, MCCC1, MCCC2, MCEE, MFN2,MGME1, MICU1, MLH1, MLYCD, MMAB, MMACHC, MMADHC, MOCS1, MPC1, MPV17,MRPL12, MRPL3, MRPL44, MRPS16, MRPS22, mt-12S rRNA, mt-tRNATyr,mt-tRNATrp, mt-tRNAVal, mt-tRNAThr, mt-tRNASer1, mt-tRNASer2,mt-tRNAArg, mt-tRNAG1n, mt-tRNAPro, mt-tRNAAsn, mt-tRNAMet, mt-tRNALeu1,mt-tRNALeu2, mt-tRNALys, mt-tRNAIle, mt-tRNAHis, mt-tRNAGly, mt-tRNAPhe,mt-tRNAGlu, mt-tRNAAsp, mt-tRNACys, mt-tRNAAla, MTFMT, MTO1, MTPAP, MUT,MUTYH, NAGS, NARS2, NCOA4, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA1,NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2,NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB11, NDUFB3, NDUFB9, NDUFS1,NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1,NNT, NUBPL, OAT, OGDH, OGG1, OPA1, OPA3, OTC, OXCT1, PAM16, PANK2,PARK7, PARS2, PC, PCCA, PCCB, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1,PDSS2, PET100, PEX11B, PEX6, PHYH, PINK1, PNPO, PNPT1, POLG, POLG2,PPM1K, PPOX, PRODH, PTRH2, PTS, PUS1, PYCR1, QDPR, RARS, RARS2, RMND1,RPL35A, RPS14, RRM2B, SARS2, SCO1, SCO2, SCP2, SDHA, SDHAF1, SDHAF2,SDHB, SDHC, SDHD, SECISBP2, SERAC1, SFXN4, SLC16A1, SLC19A3, SLC25A1,SLC25A12, SLC25A13, SLC25A15, SLC25A19, SLC25A20, SLC25A22, SLC25A3,SLC25A38, SLC25A4, SNAP29, SOD1, SPG7, SPR, SPTLC2, STAR, SUCLA2,SUCLG1, SUOX, SURF1, TACO1, TARS2, TAZ, TCIRG1, TIMM8A, TK2, TMEM126A,TMEM70, TMLHE, TPI1, TRIT1, TRMU, TRNT1, TSFM, TTC19, TUBB3, TUFM, TYMP,UNG, UQCR10, UQCRB, UQCRC2, UQCRQ, VARS2, WDR81, WFS1, XPNPEP3, andYARS2.

In some examples, the mitochondrial disorder is characterized by a pointmutation in the mitochondrial DNA (mtDNA), deletion within the mtDNA,duplication within the mtDNA, or depletion of the mtDNA.

In some examples, the mitochondrial disorder is characterized by abiochemical deficiency of respiratory chain Complex I, II, III, IV, V,or a combination thereof.

In some examples, the mitochondrial disorder is Kearns-Sayre syndrome(KSS), Leber's hereditary optic neuropathy (LHON), myoclonic epilepsyragged red fiber syndrome (MERRF), mitochondrial encephalopathy, lacticacidosis, and stroke (MELAS) syndrome, sensory ataxic neuropathy,dysarthria, and ophthalmoparesis (SANDO) syndrome, maternally inheritedLeigh syndrome (MILS), myopathy and external ophthalmoplegia,neuropathy, gastrointestinal encephalopathy (MNGIE) syndrome, Leighsyndrome, maternally inherited diabetes and deafness (MIDD) syndrome,Alpers-Huttenlocher syndrome, Sengers syndrome, mitochondrial myopathy,lactic acidosis and sideroblastic anemia (MLASA), chronic progressiveexternal ophthalmoplegia (CPEO), autosomal dominant progressive externalophthalmoplegia (AdPEO), neuropathy, ataxia, retinitis pigmentosa (NARP)syndrome, GRACILE syndrome, diabetes insipidus, diabetes mellitus, opticatrophy, and deafness (DIDMOAD) syndrome, or Pearson's syndrome.

In some examples, the mitochondrial disorder presents with one or moreof gray matter disease, white matter disease, seizures, migraines,ataxia, stroke, stroke-like episodes, deafness, optic neuropathy,peripheral neuropathy, retinopathy, external opthalmoplegia, liverfailure, kidney failure, pancreatic exocrine dysfunction, intestinalpseudoobstruction, anemia, skeletal muscle myopathy, cardiomyopathy,cardiac conduction defects, short stature, hypogonadism, immunedysfunction, or metabolic acidosis.

In some examples, the mitochondrial disorder is diagnosed by analgorithm selected from the group consisting of the Bernier criteria(Bernier et al., “Diagnostic criteria for respiratory chain disorders inadults and children,” Neurology, 59(9):1406-11, 2002), the Moravacriteria (Morava et al., “Mitochondrial disease criteria: diagnosticapplications in children,” Neurology, 67(10):1823-6, 2006), andConsensus from the Mitochondrial Medicine Society (Parikh et al.,“Diagnosis and management of mitochondrial disease: a consensusstatement from the Mitochondrial Medicine Society,” Genetics inMedicine, 17(9):689-701, 2015).

In some examples, the mitochondrial disorder is a mitochondrialrespiratory chain disorder.

In some embodiments, the subject is less than five years of age (e.g.,less than one year of age).

In any of the methods described herein, the subject optionally has anage-associated disorder (e.g., type 2 diabetes, insulin resistance,neurodegeneration, peripheral neuropathy, sarcopenia, muscle atrophy,deafness, atherosclerosis, cardiovascular disease, heart failure,chronic kidney disease, cancer, arthritis, cataracts, or osteoporosis).

In any of the methods described herein, including but not limited to acombination treatment with nitric oxide, xenon, or an agent that reducespulmonary hypertension, the subject can be treated to prevent(completely or partially) the occurrence of mitochondrial dysfunctionassociated with aging. In these embodiments, the subject can be, forexample, at least 20 years of age, at least 30 years of age, at least 40years of age, or older. In these preventative methods, the subject canbenefit from treatment even without having any evident disease. Forexample, a subject can be administered by inhalation a therapeuticallyeffective amount of a therapeutic gas comprising (i) between 5 to 20%O₂, and (ii) nitric oxide (e.g., an amount of nitric oxide disclosedherein). In another example, a subject can breathe a therapeuticallyeffective amount of air in a hypobaric chamber in combination withinhalation of nitric oxide (e.g., an amount of nitric oxide disclosedherein).

In any of the methods described herein, the subject optionally exhibitsmitochondrial dysfunction associated with aging (e.g., the subject is atleast 65 years of age or is at least 75 years of age).

In any of the methods described herein, the mitochondrial dysfunctionoccurs in response to an environmental insult (e.g., a drug, anantibiotic, an antiviral drug, or a pesticide that is toxic tomitochondria.

In any of the methods described herein, the subject can be beenidentified as having a genetic mutation associated with onset of amitochondrial disorder and treatment is initiated before the onset ofsymptoms of the disorder. For example, the subject can be identified ashaving a mutation in a gene selected from the group consisting of AARS2,AASS, ABAT, ABCB6, ABCB7, ABCD1, ACACA, ACAD8, ACAD9, ACADM, ACADS,ACADSB, ACADVL, ACAT1, ACO2, ACSF3, ACSL4, ADCK3, ADCK4, AFG3L2, AGK,AGXT, AIFM1, AK2, ALAS2, ALDH18A1, ALDH2, ALDH3A2, ALDH4A1, ALDH5A1,ALDH6A1, ALDH7A1, AMACR, AMT, APOPT1, ATIC, ATP5A1, ATPSE, ATP6, ATP8,ATPAF2, ATXN2, AUH, BAX, BCKDHA, BCKDHB, BCKDK, BCS1L, BOLA3, C10orf2,C12orf65, CASA, CARS2, CASP8, CAT, CEP89, CHCHD10, CISD2, CLPB, CLPP,COA5, COA6, COASY, COQ2, COQ4, COQ6, COQ9, COX1, COX10, COX14, COX15,COX2, COX20, COX3, COX4I2, COX6A1, COX6B1, COX7B, CPDX, CPS1, CPT1A,CPT2, CYBSA, CYB5R3, CYC1, CYCS, CYP11A1, CYP11B2, CYP24A1, CYP27A1,CYP27B1, CYTB, D2HGDH, DARS2, DBT, DGUOK, DHCR24, DHODH, DHTKD1, DIABLO,DLAT, DLD, DMGDH, DMPK, DNA2, DNAJC19, DNM1L, EARS2, ECHS1, ELAC2, ETFA,ETFB, ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FECH, FH, FKBP10, FOXRED1,FXN, GARS, GATM, GCDH, GCSH, GDAP1, GFER, GFM1, GK, GLDC, GLRX5, GLUD1,GLYCTK, GPI, GPX1, GRHPR, GTPBP3, HADH, HADHA, HADHB, HARS2, HCCS,HIBCH, HK1, HMBS, HMGCL, HMGCS2, HOGA1, HSD17B10, HSD17B4, HSPD1, HTRA2,IDH2, IDH3B, ISCA2, ISCU, IVD, KARS, KIF1B, KRT5, L2HGDH, LARS2, LIAS,LONP1, LRPPRC, LYRM4, LYRM7, MAOA, MARS2, MCCC1, MCCC2, MCEE, MFN2,MGME1, MICU1, MLH1, MLYCD, MMAB, MMACHC, MMADHC, MOCS1, MPC1, MPV17,MRPL12, MRPL3, MRPL44, MRPS16, MRPS22, mt-12S rRNA, mt-tRNATyr,mt-tRNATrp, mt-tRNAVal, mt-tRNAThr, mt-tRNASer1, mt-tRNASer2,mt-tRNAArg, mt-tRNAG1n, mt-tRNAPro, mt-tRNAAsn, mt-tRNAMet, mt-tRNALeu1,mt-tRNALeu2, mt-tRNALys, mt-tRNAIle, mt-tRNAHis, mt-tRNAGly, mt-tRNAPhe,mt-tRNAGlu, mt-tRNAAsp, mt-tRNACys, mt-tRNAAla, MTFMT, MTO1, MTPAP, MUT,MUTYH, NAGS, NARS2, NCOA4, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA1,NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2,NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB11, NDUFB3, NDUFB9, NDUFS1,NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1,NNT, NUBPL, OAT, OGDH, OGG1, OPA1, OPA3, OTC, OXCT1, PAM16, PANK2,PARK7, PARS2, PC, PCCA, PCCB, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1,PDSS2, PET100, PEX11B, PEX6, PHYH, PINK1, PNPO, PNPT1, POLG, POLG2,PPM1K, PPDX, PRODH, PTRH2, PTS, PUS1, PYCR1, QDPR, RARS, RARS2, RMND1,RPL35A, RPS14, RRM2B, SARS2, SCO1, SCO2, SCP2, SDHA, SDHAF1, SDHAF2,SDHB, SDHC, SDHD, SECISBP2, SERAC1, SFXN4, SLC16A1, SLC19A3, SLC25A1,SLC25A12, SLC25A13, SLC25A15, SLC25A19, SLC25A20, SLC25A22, SLC25A3,SLC25A38, SLC25A4, SNAP29, SOD1, SPG7, SPR, SPTLC2, STAR, SUCLA2,SUCLG1, SUOX, SURF1, TACO1, TARS2, TAZ, TCIRG1, TIMM8A, TK2, TMEM126A,TMEM70, TMLHE, TPI1, TRIT1, TRMU, TRNT1, TSFM, TTC19, TUBB3, TUFM, TYMP,UNG, UQCR10, UQCRB, UQCRC2, UQCRQ, VARS2, WDR81, WFS1, XPNPEP3, andVARS2.

Examples of oxidative stress disorders that can be treated according tothe methods described herein include Parkinson's disease, Alzheimer'sdisease, amyotrophic lateral sclerosis, Huntington's disease, multiplesclerosis, Asperger syndrome, attention deficit hyperactivity disorder,diabetes, cardiovascular disease, cancer, Lafora disease,atherosclerosis, heart failure, myocardial infarction, fragile Xsyndrome, sickle cell disease, lichen planus, vitiligo, and autism.

Examples of inflammatory disorders that can be treated according to themethods described herein include rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, inflammatory bowel disease (e.g.,ulcerative colitis and Crohn's disease), psoriasis, inflammatorymyositis, Langerhans-cell histiocytosis, adult respiratory distresssyndrome, Wegener's granulomatosis, vasculitis, cachexia, stomatitis,idiopathic pulmonary fibrosis, dermatomyositis, polymyositis,non-infectious scleritis, chronic sarcoidosis with pulmonaryinvolvement, myelodysplastic syndrome, moderate to severe chronicobstructive pulmonary disease without significant right to left shuntingof blood, and giant cell arteritis.

In another aspect, the disclosure provides a system comprising (i) anenclosed tent or chamber or a breathing apparatus, (ii) a hypoxiainduction system that delivers oxygen-depleted air to the enclosed tentor chamber or the breathing apparatus, wherein the oxygen-depleted aircomprises between 5 to 20% O₂, and (iii) a device (e.g., pulse oximeter)that measures arterial oxygen saturation in a subject breathing airwithin the enclosed tent or chamber or from the breathing apparatus,wherein the system adjusts the oxygen content of the oxygen-depleted airdelivered to the enclosed tent or chamber or the breathing apparatusbased upon the oxygen saturation measured by the device such that oxygensaturation in the subject is maintained within the range of 50% to 90%(e.g., within the range of 80% to 90% or at about 85%, or within therange of 55% to 65% or at about 80%). In some embodiments, the hypoxiainduction system comprises a first container comprising a first gascomprising nitrogen and a second container comprising a second gascomprising oxygen, and wherein the oxygen-depleted air delivered to theenclosed tent or chamber or the breathing apparatus is prepared bymixing the first gas and the second gas. In some embodiments, thehypoxia induction system intakes ambient air, reduces the oxygen contentof the intake air, to produce the oxygen-depleted air that is deliveredto the enclosed tent or chamber or the breathing apparatus. In someembodiments, the hypoxia induction system intakes ambient air, addsnitrogen to the intake air, to produce the oxygen-depleted air that isdelivered to the enclosed tent or chamber or the breathing apparatus.

In any of the embodiments described herein, the subject can be a humansubject.

In a further aspect, the disclosure provides a method of screening for acompound that increases the activity of a hypoxia response comprising

a) administering a candidate compound to a first set of one or morecells with a compromised function of the mitochondrial respiratorychain;

b) measuring the growth of the first set of one or more cells; and

c) comparing the growth of the first set of one or more cells to thegrowth of a second set of one or more cells, wherein the second set ofone or more cells also have compromised function of the mitochondrialrespiratory chain, but have not been administered the candidatecompound,

wherein if the growth of the first set of cells is greater than thegrowth of the second set of cells then the candidate compound increasesthe activity of a hypoxia response.

In another aspect, the disclosure provides a method of screening fortargets for the modulation of mitochondrial respiratory chain functioncomprising

a) administering to a first set of one or more cells one or more sgRNAstargeting at least one gene in the human genome;

b) compromising the function of the mitochondrial respiratory chain inthe first set of one or more cells;

c) measuring the growth of the first set of one or more cells; and

d) comparing the growth of the first set of one or more cells to thegrowth of a second set of one or more cells, wherein the second set ofone or more cells have been administered the same one or more sgRNAs,but have less compromised function of the mitochondrial respiratorychain,

-   -   wherein if the relative enrichment of a sgRNA in the first set        of cells is greater than the corresponding enrichment in the        second set of cells then the gene is a target for the modulation        of cellular or whole body response to mitochondrial respiratory        chain (dys)function.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic representation of hypoxia.

FIG. 2 shows a schematic representation of normoxia.

FIG. 3 shows a schematic representation of the effect of Antimycin onthe mitochondrial respiratory chain.

FIG. 4 shows a schematic representation of the CRISPR screen, whereincells were divided into groups of untreated (U), moderate (M), andsevere (S).

FIG. 5 shows the relative growth of cells in a mitochondrial respiratorychain disorder model.

FIG. 6 shows sgRNA enrichment in disease conditions relative topre-treatment conditions highlighting VHL sgRNAs.

FIG. 7 shows sgRNA enrichment in disease conditions relative topre-treatment conditions as a log plot.

FIG. 8 shows sgRNA enrichment in disease conditions relative topre-treatment conditions.

FIG. 9 shows sgRNA enrichment in disease conditions relative topre-treatment conditions as a log plot.

FIG. 10 shows relative cell count with VHL sgRNA comparing untreated (U)to treated conditions (early, E; moderate, M; and severe, S) in K562cells.

FIG. 11 shows relative cell count with VHL sgRNA comparing untreated totreated conditions in K562 cells.

FIG. 12 shows relative cell count with VHL sgRNA comparing untreated totreated conditions in K562 cells.

FIG. 13 shows relative cell count with VHL sgRNA comparing untreated totreated conditions in HEK 293 cells.

FIG. 14 shows HIF1a stabilization in the face of mitochondrialdysfunction during states of normoxia or hypoxia with FG-4592.

FIG. 15 shows upregulated transcription of exemplary genes involved inenergy metabolism with FG-4592.

FIG. 16 shows time-dependent increase in activation of the hypoxiaresponse in reporter fish, upon addition of an PHD inhibitor.

FIG. 17 shows survival of zebrafish with respiratory chain inhibitors ina model of mitochondrial respiratory chain disorder.

FIGS. 18A-F show that chronic hypoxic breathing (11% O₂) preventsneurological disease symptoms and pathology in a mouse model of Leighsyndrome, whereas a few days of breathing mild hyperoxia (55% O₂) islethal and produces fatal pulmonary edema. (A) Ndufs4 KO mice of bothgenders were chronically exposed to hypoxic breathing at normobaria (11%O₂; top line), normoxia (21% O₂; middle line), or hyperoxia (55% O₂;bottom line) at 30 days of age and survival was recorded (n=12, n=12,n=9 mice, respectively). (B) Body weights were measured in WT and KOmice exposed to normoxia or hypoxia, three times a week upon enrollmentin the study. Weights are shown as mean±S.E. (C) Representative imagesof 50 day-old KO mice exposed to normoxia or hypoxia. (D) Bodytemperature was measured in KO mice exposed to normoxia or hypoxia atapproximately age 30 days, 40 days, and 50 days. Temperatures are shownas mean±S.E. (E) Latency to fall on an accelerating rod was measured asmedian values of triplicate trials per mouse for WT and KO mice, exposedto normoxia or hypoxia at different ages. (F) Representative 1 hourlocomotor activity traces of sick, normoxia-treated KO mice, andage-matched hypoxia-treated KO mice, as well as controls. *denotest-test p-value <0.05.

FIGS. 19A-E show that therapeutic hypoxic breathing (11% O₂) by Ndufs4KO mice prevents the appearance of metabolic disease markers, as well asneuropathology, without rescuing Complex I activity. (A) Hematocritvalues for WT and KO mice treated with normoxia or hypoxia at normobariafor approximately 3 weeks (n=3-4 per group). (B) Complex I activity inKO mice relative to WT mice, in both normoxic and hypoxic conditions(n=3-4 per group). (C) Representative images for immunostaining againstthe inflammatory marker, Iba-1, in the olfactory bulb and cerebellum ofNdufs4 KO mice treated with hypoxia or normoxia and WT mice exposed tonormoxic breathing. (D) Plasma α-hydroxybutyrate levels in WT and KOmice, exposed to hypoxia or normoxia (n=4-8 per group). Median shown ashorizontal bar. (E) Plasma lactate in WT and KO mice, exposed to hypoxiaor normoxia (n=4-8 per group). Median shown as horizontal bar.

FIG. 20 shows spontaneous activity measured in WT and Ndufs4 KO miceexposed to normoxia or hypoxia. Distance travelled and jump countswithin 1 hour are shown (Mean±S.E.). n=7, 5, 9, 9 for WT (21% O₂), WT(11% O₂), KO (21% O₂), KO (11% O₂) respectively.

FIGS. 21A-D show that hypoxic breathing (11% O₂) rescues mice withsevere neurological disease, and enables long term survival, augmentsbody weight and enhances the behavior of Ndufs4 KO mice who havedeveloped late-stage neurologic impairment. (A) Growth curves of Ndufs4KO female mice exposed to therapeutic hypoxic breathing, starting at 30days of age (triangles) and late-stage hypoxic breathing, starting at 55days of age (circles). (B) Body temperature and (C) latency of fallingfrom an accelerating rod in Ndufs4 KO mice with late-stage disease andWT controls exposed to breathing 11% O₂ starting at 55 days of age. (D)Survival rates of mice in normoxia (unbroken lines) or hypoxia beginninglate-stage disease (dashed lines). Data shown as mean±SE.

FIG. 22 displays a series of photographs showing that breathing 11% O₂reverses the established neurological lesions of Ndufs4 KO mice who werebreathing air. Four Ndufs4 KO mice breathed normoxic air (21% O₂) untilthey developed late-stage debilitating neurological disease (55 days).MRI scans were performed and detected hyperintense lesions, apparent inthe vestibular nuclei (top row, white arrows). Subsequently, micebreathed 11% oxygen and were scanned again at two and four weeks afterhypoxic treatment (middle and bottom rows respectively). Neurologicallesions on MRI had disappeared by four weeks of hypoxic breathing.

FIGS. 23A-B are a series of photographs showing the absence ofneurodegenerative pathology in 250 day old hypoxia-treated Ndufs4 KOmice. (A) Representative images with staining of the microglialactivation marker, Iba-1. Normoxic breathing Ndufs4 KO mice at 50 dayshave a significant inflammatory response in the cerebellum and olfactorybulb. Analogous images in 250 day old hypoxic Ndufs4 KO mice and WT micedo not show brain inflammation. (B) Axial MRI head scans showingbilateral, symmetric hyperintense lesions in the vestibular nucleus andolfactory bulbs of normoxic Ndufs4 KO mice. These lesions were notpresent in chronically hypoxic Ndufs4 KO mice at 250 days of age.

FIGS. 24A-E show depressed myocardial function in Ndufs4 KO micebreathing 11% 02 at 250 days. (A) Left ventricular fractional shortening(FS %) of six mice breathing different oxygen concentrations at 50 daysof age. (B) FS % of six mice breathing various oxygen concentrations at250 days of age. (C) Left ventricular cavity interior diastolic diameter(LVID) at 250 days of age. (D) Left ventricular interior systolicdiameter (LVIS) of six mice at 250 days of age. (E) RepresentativeM-mode scans of the left ventricle in WT and KO mice breathing 11% 02 at250 days. Scans were obtained during light sedation with isofluranewhile breathing 21% 02. Data mean±SE; *p<0.05 vs WT; #p<0.05 vs WT 11%.

FIGS. 25A-F show that intermittent hypoxic (11%) breathing (10 h/day)did not alleviate mitochondrial disease. (A) Survival rates for Ndufs4KO mice breathing different oxygen levels and intermittent hypoxicbreathing for 10 h/day (IH). IH versus normoxia, log rank p=0.77, HR1.13 (0.48-2.79). (B) Body weights after breathing different oxygenlevels and during intermittent hypoxic breathing starting at 30 d ofage. (C) Body temperature and (D) latency to fall from an accelerating,rotating rod for Ndufs4 KO mice breathing various oxygen levels orreceiving intermittent hypoxia starting at 30 days of age. (E)Hematocrit levels for WT and Ndufs4 KO mice following three weeks ofexposure to normoxia, hypoxia or intermittent hypoxic breathing. (F)Representative MRI of a 65d Ndufs4 KO mouse exposed to intermittenthypoxic breathing. Arrows denote lesions in vestibular nuclei. Datamean±SE; *p<0.05 vs KO 11% O₂; #p<0.05 vs KO 21% O₂.

FIGS. 26A-D shows that breathing moderate hypoxia (17% O₂) does notalleviate murine mitochondrial disease. (A) Survival rates for Ndufs4 KOmice breathing at different oxygen levels starting at 30 days of age.(B) Time course of body weight (n=6, each group) and (C) bodytemperature for 17% oxygen exposure, compared to 21% or 11% oxygenexposure for 30, 40 and 50 days. (D) Venous hematocrit after three weeksof exposure to different oxygen levels. Data mean±SE; *p<0.05 differs vs11% oxygen, # p<0.05 differs vs 17% oxygen.

FIGS. 27A-B show that hypoxia and nitric oxide combination therapyimproves behavioral performance. (A) Survival curve for Ndufs4 KO micebreathing normoxia, hypoxia or hypoxia combined with low-dose NO(ordering of lines from top to bottom at right side of graph: KO,hypoxia+NO; KO, hypoxia; KO, normoxia). (B) Rotarod test for muscle andgrip strength in WT and KO mice exposed to normoxia or hypoxia, with orwithout nitric oxide. Data mean±SE.

FIGS. 28A-B show that hypoxia is protective against low-dose LPSsensitivity of Ndufs4 KO mice. (A) Survival curve for Ndufs4 KO micebreathing hypoxia or normoxia after i.p. injection of LPS (5 mg/kg), awell-tolerated dose in WT mice (ordering of lines from top to bottom atright side of graph: KO, hypoxia; KO, normoxia). (B) Core temperature inWT and KO mice exposed to either hypoxia or normoxia after low-dose LPSinjection (ordering of lines from top to bottom at right side of graph:WT, normoxia; WT, hypoxia; KO, normoxia; KO, hypoxia).

DETAILED DESCRIPTION

The disclosure provides a method of treating or preventing mitochondrialdysfunction, an oxidative stress disorder, or an inflammatory disorderin a subject in need thereof comprising increasing the activity of thehypoxia response pathway in the subject. In some embodiments, the methodcomprises suppression of mitochondrial disease. In certain embodiments,the suppression of mitochondrial disease occurs via mediation of thehypoxia response.

The disclosure also provides methods of screening for compounds thattreat or prevent mitochondrial dysfunction, an oxidative stressdisorder, or an inflammatory disorder. In some embodiments, methods ofscreening for a compound that increases the activity of a hypoxiaresponse is provided. In other embodiments, methods of screening fortargets for the modulation of response to mitochondrial respiratorychain dysfunction are provided.

A. Terms, Definitions and Abbreviations

As used herein “hypoxia” refers to a deficiency of oxygen. A low oxygencondition is also referred to as a “hypoxic condition.” See FIG. 1 for aschematic representation of hypoxia. HIF1α is stabilized during hypoxia.

As used herein a “hypoxia inducible transcription factor” (HIF) is anoxygen-sensitive transcription factor that responds to low oxygen.Non-limiting examples of hypoxia inducible transcription factors includealpha subunits of hypoxia inducible transcription factors (e.g., HIF1a,HIF2 α and HIF3α), and beta subunits (HIF1β, HIF2β, and HIF3β). HIFs arealso referred to herein as HIF proteins. For example, in atranscriptional complex HIF is a heterodimer comprising an alpha and abeta subunit, which induces transcription of HIF-responsive genes duringhypoxia or under hypoxic conditions.

HIF-responsive genes include but are not limited to genes involved inglucose metabolism, for example, transport (e.g., glucose transporter 1(GLUT1) and glucose transporter 3 (GLUT3)), tricarboxylic acid (TCA)cycle (also known as the Krebs cycle or the citric acid cycle, e.g.,PDK1), glycolysis (e.g., hexokinase 1 (HK1); hexokinase 2 (HK2);glyceraldehyde 3-phosphate dehydrogenase (GAPDH);6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKBF3);6-phosphofructo-2-kinase, liver type (PFKL); phosphoglycerate kinase 1(PGK1); and pyruvate kinase, muscle (PKM)); redox modulation (e.g.,lactate dehydrogenase A (LDHA) and monocarboxylate transporter 4(MCT4)); feedback regulation (e.g., Egl-9 family hypoxia-induciblefactor 1 (EGLN1) and Egl-9 family hypoxia-inducible factor 3 (EGLN3));angiogenesis (e.g., vascular endothelial growth factor (VEGF); vascularendothelial growth factor receptor (VEGFR); endoglin (ENG); transforminggrowth factor, beta 3 (TGF-B3); adrenomedullin (ADM); nitric oxidesynthase 2, inducible (NOS2); heme oxygenase 1 (HMOX1)); and promotingred blood cell maturation and oxygen transport, for example,erythropoiesis (e.g., erythropoietin (EPO)) and iron metabolism (e.g.,transferrin (TF) and transferrin receptor (TFRC)). Other examples ofHIF-responsive genes include the genes disclosed in J. Med. Chem. 56,9369-9402 (2013), incorporated herein by reference in its entirety.

A “hypoxia response” is a response by a cell and/or an organism tohypoxia. Hypoxia is one non-limiting way to induce a hypoxia response. Ahypoxia response includes, but is not limited to, a physiologicalresponse (e.g., a systemic or pulmonary hemodynamic response, a changein the regulation of cellular metabolism, and up-regulation of genes(e.g., HIF responsive genes)) and a pathological response (e.g.,pulmonary hypertension, cerebral ischemia, myocardial ischemia, andtumor angiogenesis). Non-limiting examples of systemic responses includepulmonary vasoconstriction, systemic vasodilation, increased cytosoliccalcium concentration, and neurotransmitter release, for example,catecholamines, acetylcholine, and serotonin. Non-limiting examples of aresponse affecting the regulation of cellular metabolism includeuncontrolled cell swelling, cell necrosis, impaired mitochondrialrespiratory chain function, increased cellular glycolysis, decreasedcellular energy consumption, and decreased cellular oxygen consumption.Other examples of a hypoxia response include increased ventilation,increased cardiac output, a switch from aerobic to anaerobic metabolism,promotion of improved vascularization, an increase of erythropoietinwith augmented erythropoiesis, enhancement of the oxygen carryingcapacity of the blood, reduced oxygen toxicity, increased or reducedreactive oxygen species, and increased or reduced oxidative stress. Ahypoxia response may involve oxygen-responsive pathways to sense and torespond to changes in oxygen availability. For example, HIFs may respondto a low oxygen environment and activate one or more HIF-responsivegenes.

Normoxia or a “normoxic condition” refers to a normal level of oxygencondition. See FIG. 2 for a schematic representation of normoxia. HIF1αis degraded under normoxic conditions.

The “prolyl-hydroxylase” (PHD) enzymes hydroxylate alpha subunits of HIFat conserved proline residues. Hydroxylation and degradation occursunder normoxic conditions. PHD enzyme activity is inhibited underhypoxic conditions. Non-limiting examples of PHD inhibitors include2-oxoglutarate analogs (also known as α-ketoglutarate, e.g., roxadustat,2,4-diethylpyridine dicarboxylate, dimethyloxallyl glycine, IOX2, andN-oxalylglycine), β-oxocarboxylic acids (e.g.,1,4-dihydrophenonthrolin-4-one-3-carboxylic acid), and BAY-85-3934 (alsoknown as2-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1,2-dihydro-3H-pyrazol-3-one).Roxadustat is also known as FG-4592 andN-[(4-hydroxy-1-methyl-7-phenoxy-3-isoquinolinyl)carbonyl]glycine. IOX2is also known as(1-benzyl-4-hydroxy-2-oxo-1,2-dihydroquinoline-3-carbonyl)glycine.Additional examples of 2-oxoglutarate analogs as PHD inhibitors include4-hydroxyisoquinoline-2-carbonylglycine derivatives,4-hydroxy-2-quinoline, pyrrolopyridines, thiazolopyridines,isothiazolopyridines, 4-hydroxycoumarins, and 4-hydroxythiocoumarins(11). For example, FG-2216((1-chloro-4-hydroxyisoquinoline-3-carbonyl)glycine) and FG-4497((1-hydroxy-6-(phenylthio)isoquinoline-3-carbonyl)glycine). Any knownprolyl-hydroxylase inhibitor may be used in methods of the invention.Some additional examples of PHD inhibitors are disclosed in M.Rabinowitz, Inhibition of hypoxia-inducible factor prolyl hydroxylasedomain oxygen sensors: tricking the body into mounting orchestratedsurvival and repair responses. J. Med. Chem. 56, 9369-9402 (2013),incorporated herein by reference in its entirety.

The “Von Hippel Lindau” gene encodes the Von Hippel Lindau (VHL) tumorsuppressor protein. The hydroxylated form of HIF is recognized by theubiquitin ligase, VHL, and targeted for degradation by the proteasomeunder normoxic conditions.

As used herein, “endogenous cellular oxygen sensing” involves amechanism or process used by the body or cells to determine or tomeasure the levels of oxygen available to the cells. For example, oxygensensing may occur using a hypoxia response.

As used herein, a “mitochondrial respiratory chain disorder” is aheterogeneous group of genetic disorders that share involvement of thecellular bioenergetics machinery due to molecular defects affecting themitochondrial oxidative phosphorylation system. Over 150 differentgenetic causes of mitochondrial respiratory chain disorder impact one ormore of the five respiratory chain complexes. The respiratory chaincomplexes include Complex I (NADH-coenzyme Q reductase or NADHdehydrogenase), Complex II (succinate-coenzyme Q reductase or succinatedehydrogenase), Complex III (cytochrome bci complex or coenzymeQ-cytochrome C oxidoreductase), Complex IV (cytochrome C oxidase), andComplex V (ATP synthase, adenosine triphosphate synthase). Amitochondrial lesion is damage to a gene encoded by mitochondrial DNA ornuclear-encoded mitochondrial protein. The mitochondrial lesion may beintroduced by oxidative stress. Mitochondrial diseases include amitochondrial respiratory chain disorder.

A “Complex I inhibitor” inhibits the functioning of the NADH-coenzyme Qreductase in the mitochondrial electron transport chain and preventselectron transfer from NADH to coenzyme Q10. Non-limiting examples of aComplex I inhibitor include acetogenins (e.g., annonacin, bullatacin orrolliniastatin-2, and uvaricin), reduced nicotinamide adeninedinucleotide (NADH) analogs (e.g., adenosine diphosphate ribose),ubiquinone analogs (e.g., piericidin (also referred to as piericidin A)and rotenone), and metformin.

A “Complex III inhibitor” inhibits the functioning of the coenzymeQ-cytochrome C oxidoreductase in the mitochondrial electron transportchain and prevents the biochemical generation of ATP. Non-limitingexamples of a Complex III inhibitor include Q_(i) site inhibitors (e.g.,antimycin) and Q_(o) site inhibitors (quinone outside inhibitors, e.g.,myxothiazol, stigmatellin, and strobilurin derivatives).

A “Complex V inhibitor” inhibits the functioning of ATP synthase in themitochondrial electron transport chain and prevents the biochemicalgeneration of ATP. Non-limiting examples of a Complex V inhibitorinclude α-helical basic peptide inhibitors (e.g., melittin), catechins(e.g., epicatechin, epicatechin gallate, and epigallocatechin gallate),catecholestrogens (e.g., 4-hydroxyestradiol and 2-hydroxyestradiol),flavones (e.g., quercetin, morin, kaempferol, and genistein),oligomycins (e.g., oligomycin A and oligomycin), polyketide inhibitors(e.g., peliomycin, venturicidin A, B, and X, and ossamycin), stilbenes(e.g., resveratrol, piceatannol, and diethylstilbestrol), tentoxin andderivatives (e.g., tentoxin), and nucleotide analogs (e.g., GTP, FTP,and TNP-ATP). A Complex V inhibitor is also referred to as an ATPsynthase inhibitor.

A “compromised function of the mitochondrial respiratory chain” refersto one or more cells with abnormal functioning of the cellularbioenergetics machinery affecting the mitochondrial oxidativephosphorylation system. For example, this may be a result of geneticdefects in one or more respiratory chain complexes, a mitochondriallesion, an inhibitor of one or more respiratory chain complexes or anyphysiological situation which impairs mitochondrial respiratory chainfunction.

As used herein, “basal respiration” refers to routine respiration in anintact and healthy cell. The proton current generated by basalrespiration supplies ATP synthesis and the proton leak.

As used herein, “cellular stress” may be caused by environmentalstressors including temperature extremes, toxin exposure, mechanicaldamage, and hypoxic conditions. For example, viral prodromes,dehydration, and low oxygen cause cellular stress. When a cell isexposed to unfavorable environmental conditions of cellular stress, thecell can mount a response to protect the cell against the environmentalstressors.

A “high energy demand” requires the cell to produce a large amount ofenergy to perform required functions. For example, mitochondria areorganelles that carry out the process of aerobic respiration tobreakdown molecules like glucose in the presence of oxygen. The cellularbioenergetics machinery uses respiratory chain complexes to produceenergy for a cell. In certain embodiments, high energy demand occurs incells when an organism comprising those cells exerts itself beyond asedentary condition. In other embodiments, high energy demand occurswhen an organism comprising the cells is injured in a location near thecells. In other embodiments, high energy demand occurs when an organismcomprising the cells is suffering from an infectious disease thataffects the cells.

An “age-associated disorder” is a disease or a disorder seen withincreasing frequency as individuals age. These disorders are associatedwith gradual deterioration of function (e.g., quantitative decline inthe activity of the mitochondrial respiratory chain). Non-limitingexamples of an age-associated disorder include type 2 diabetes,neurodegeneration (e.g., Alzheimer's disease), sarcopenia (muscle loss),atherosclerosis, cardiovascular disease, cancer, arthritis, cataracts,and osteoporosis.

“CRISPR” is a clustered regularly interspaced short palindrome repeatguided by RNA to introduce a targeted loss-of function mutation at oneor more specific sites in the genome. The system includes a sgRNA and anendonuclease such as the CRISPR associated protein 9 (Cas9) nuclease.Various compositions and methods of use related to the delivery,engineering, optimization and therapeutic applications of systems,methods, and compositions used for the control of gene expressioninvolving sequence targeting, such as genome perturbation orgene-editing, may be utilized in the invention. In one aspect, thegenome perturbation or gene-editing relates to Clustered RegularlyInterspaced Short Palindromic Repeats (CRISPR) and components thereof.The CRISPR-Cas system does not require the generation of customizedproteins to target specific sequences but rather a single Cas enzyme canbe programmed by a short RNA molecule to recognize a specific DNAtarget. Examples of useful CRISPR-Cas systems and components include,but are not limited to, the components, or any corresponding orthologsthereof, and delivery of such components, including methods, materials,delivery vehicles, vectors, particles, AAV, and making and usingthereof, as described in, e.g., US Patents Nos. 8 U.S. Pat. No.8,697,359, U.S. Pat. No. 8,771,945, U.S. Pat. No. 8,795,965, U.S. Pat.No. 8,865,406, U.S. Pat. No. 8,871,445, U.S. Pat. No. 8,889,356, U.S.Pat. No. 8,889,418, U.S. Pat. No. 8,895,308, U.S. Pat. No. 8,906,616,U.S. Pat. No. 8,932,814, U.S. Pat. No. 8,945,839, U.S. Pat. No.8,993,233 and U.S. Pat. No. 8,999,641 and applications related thereto;and PCT Patent Publications WO2014/018423, WO2014/093595, WO2014/093622,WO2014/093635, WO2014/093655, WO2014/093661, WO2014/093694,WO2014/093701, WO2014/093709, WO2014/093712, WO2014/093718,WO2014/145599, WO2014/204723, WO2014/204724, WO2014/204725,WO2014/204726, WO2014/204727, WO2014/204728, WO2014/204729,WO2015/065964, WO2015/089351, WO2015/089354, WO2015/089364,WO2015/089419, WO2015/089427, WO2015/089462, WO2015/089465,WO2015/089473 and WO2015/089486, and applications related thereto.

As used herein, “RNAi Gene Enrichment Ranking” (RIGER) analysis uses analgorithm to rank screening hits by the consistent enrichment amongmultiple sgRNAs targeting the same gene. The highest ranking (e.g.,lowest number, rank 1) gene represents a gene target. Additional detailsabout the algorithm can be found in B. Luo et al., Highly parallelidentification of essential genes in cancer cells. Proc. Natl. Acad.Sci. U.S.A. 105, 20380-20385 (2008), incorporated herein by reference inits entirety.

A “sgRNA” is an RNA that guides the insertion or deletion of nucleotidesinto target locations in concert with the Cas9 nuclease.

B. Embodiments

In one aspect, the current disclosure provides a method of treating orpreventing mitochondrial dysfunction, an oxidative stress disorder, oran inflammatory disorder in a subject in need thereof comprisingincreasing the activity of a hypoxia response in the subject. Increasingthe activity of a hypoxia response can be achieved by, for example,exposing the subject to hypoxia. In some embodiments, the hypoxiaresponse may include, but is not limited to, one or more of thefollowing: a physiological response (e.g., a systemic response, a changein the regulation of cellular metabolism, and up-regulation of genes(e.g., HIF responsive genes)) or a trigger of a hypoxia response (e.g.,cerebral ischemia, myocardial ischemia, and tumor angiogenesis). Inanother embodiment, the hypoxia response is a systemic or pulmonaryresponse selected from the group consisting of pulmonaryvasoconstriction, systemic vasodilation, increased cytosolic calciumconcentration, neurotransmitter release. In still another embodiment,the hypoxia response is a response affecting the regulation of cellularmetabolism selected from the group consisting of uncontrolled cellswelling, cell necrosis, impaired mitochondrial respiratory chainfunction, increased cellular glycolysis, and decreased cellular energyconsumption. In yet another embodiment, a hypoxia response is selectedfrom the group consisting of increased ventilation, increased cardiacoutput, a switch from aerobic to anaerobic metabolism, promotion ofimproved vascularization, and augmented erythropoietin levels withenhancement of erythropoiesis, enhancement of the oxygen carryingcapacity of the blood, reduced oxygen toxicity, increased or reducedreactive oxygen species, and increased or reduced oxidative stress.

In some embodiments, increasing the activity of a hypoxia responseincludes increasing the activation of a hypoxia inducible transcriptionfactor (HIF). In other embodiments, the HIF is selected from the groupconsisting of alpha or beta subunits of hypoxia inducible transcriptionfactors. In certain embodiments, the HIF is selected from the groupconsisting of HIF1α, HIF3α, HIF1β, HIF2β, HIF3β, and HIF2α.

In another embodiment, increasing the activity of a hypoxia responseincludes inducing transcription of HIF-responsive genes. In otherembodiments, the transcribed gene is involved in one of the followingglucose metabolism, glucose transport, glycolysis, redox modulation,feedback regulation, angiogenesis, promoting red blood cell maturationand oxygen transport, erythropoiesis, and iron metabolism. In someembodiments, the HIF-responsive gene is selected from the groupconsisting of glucose transporter 1 (GLUT1); glucose transporter 3(GLUT3); pyruvate dehydrogenase kinase, isozyme 1 (PDK1); hexokinase 1(HK1); hexokinase 2 (HK2); glyceraldehyde 3-phosphate dehydrogenase(GAPDH); 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3(PFKBF3); 6-phosphofructo-2-kinase, liver type (PFKL); phosphoglyceratekinase 1 (PGK1); pyruvate kinase, muscle (PKM); lactate dehydrogenase A(LDHA); monocarboxylate transporter 4 (MCT4); Egl-9 familyhypoxia-inducible factor 1 (EGLN1); Egl-9 family hypoxia-induciblefactor 3 (EGLN3); vascular endothelial growth factor (VEGF); vascularendothelial growth factor receptor (VEGFR); endoglin (ENG); transforminggrowth factor, beta 3 (TGF-B3); adrenomedullin (ADM); nitric oxidesynthase 2, inducible (NOS2); heme oxygenase 1 (HMOX1); erythropoietin(EPO); transferrin (TF); and transferrin receptor (TFRC).

In yet another embodiment, increasing the activity of a hypoxia responseis done during normoxic conditions. In some embodiments, increasing theactivity of a hypoxia response is not through stabilization oractivation of HIF1α. In still another embodiment, increasing theactivity of a hypoxia response comprises bypassing endogenous cellularoxygen sensing.

In some embodiments, the subject comprises mitochondria comprising oneor more mitochondrial lesions or other lesions which impactmitochondrial respiratory chain function. In another embodiment, the oneor more mitochondrial lesions may be introduced by oxidative stress. Inother embodiments, the one or more mitochondrial lesions occur in arespiratory chain complex. In certain embodiments, the one or moremitochondrial lesions occur in a protein complex, wherein the proteincomplex is selected from the group consisting of: Complex I, Complex II,Complex III, Complex IV, Complex V, and ATP (adenosine triphosphate)Synthase.

In other embodiments, the method comprises inhibition of one or moreproteins involved in the hypoxia response. In certain embodiments,inhibition of one or more proteins involved in a hypoxia responseincreases the activity of the hypoxia response. In some embodiments, themethod comprises inhibition of PHD or VHL protein. In anotherembodiment, the PHD inhibitor is selected from the group consisting of2-oxoglutarate analogs (also known as α-ketoglutarate), β-oxocarboxylicacids, and BAY-85-3934. In some embodiments, the PHD inhibitor isFG-4592 or roxadustat. One of skill in the art may use any PHD inhibitoror VHL inhibitor known in the art for use in methods disclosed herein.In yet another embodiment, the method comprises increasing the stabilityor the activation of hypoxia inducible transcription factor (HIF). Inanother embodiment, increasing the activity of the hypoxia responsecomprises increasing the stability or the activation of HIF proteins. Insome embodiments, increasing the stability of HIF proteins is doneduring normoxic conditions.

In yet another embodiment, the mitochondrial disorder is a geneticdisorder that affects the mitochondrial oxidative phosphorylationsystem. In some embodiments, the mitochondrial disorder affects one ormore of the five respiratory chain complexes. In certain embodiments,the respiratory chain complexes is selected from the group consisting ofComplex I (NADH-coenzyme Q reductase or NADH dehydrogenase), Complex II(succinate-coenzyme Q reductase or succinate dehydrogenase), Complex III(cytochrome bci complex or ubiquinone-cytochrome C oxidoreductase),Complex IV (cytochrome C oxidase), and Complex V (ATP synthase).

In still another embodiment, the subject has an age-associated disorder.In some embodiments, the age-associated disorder is selected from thegroup consisting of type 2 diabetes, neurodegeneration (e.g.,Alzheimer's disease), sarcopenia (muscle loss), insulin resistance,peripheral neuropathy, muscle atrophy, deafness, atherosclerosis,cardiovascular disease, heart failure, chronic kidney disease, cancer,arthritis, cataracts, and osteoporosis. In other embodiments, theage-associated disorder is selected from the group consisting of type 2diabetes, neurodegeneration and sarcopenia.

In another aspect, the current disclosure provides a method ofincreasing the activity of a hypoxia response in a subject in needthereof comprising increasing the stability or the activation of HIFproteins in the subject.

In yet another aspect, the current disclosure provides a method oftreating or preventing mitochondrial dysfunction, an oxidative stressdisorder, or an inflammatory disorder in a subject in need thereofcomprising increasing cellular glycolysis in the subject. In someembodiments, increasing cellular glycolysis comprises activation of agene involved in glycolysis. In certain embodiments, the gene involvedin glycolysis is selected from the group consisting of hexokinase 1(HK1); hexokinase 2 (HK2); glyceraldehyde 3-phosphate dehydrogenase(GAPDH); 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3(PFKBF3); 6-phosphofructo-2-kinase, liver type (PFKL); phosphoglyceratekinase 1 (PGK1); and pyruvate kinase, muscle (PKM). In otherembodiments, increasing cellular glycolysis is done during normoxicconditions. In still other embodiments, increasing cellular glycolysiscomprises bypassing endogenous cellular oxygen sensing.

In still another aspect, the current disclosure provides a method oftreating or preventing mitochondrial dysfunction, an oxidative stressdisorder, or an inflammatory disorder in a subject in need thereofcomprising suppressing cellular basal respiration in the subject. Insome embodiments, the suppressing cellular basal respiration is doneduring normoxic conditions. In other embodiments, suppressing cellularbasal respiration comprises bypassing endogenous cellular oxygensensing.

In other embodiments, the treatment using one of the methods disclosedherein is during a period of cellular stress. In certain embodiments,the period of cellular stress corresponds to hypoxic conditions. Inanother embodiment, the treatment using one of the methods disclosedherein is during a period of high energy demand. In some embodiments,the period of high energy demand uses respiratory chain complexes toproduce energy for a cell.

In some embodiments, the method of treatment or prevention ofmitochondrial dysfunction, an oxidative stress disorder, or aninflammatory disorder in a subject in need thereof is applied over aperiod of time that can range, e.g., from 8 hrs/day (sleep period) toabout 1 day to about 50 years, and more usually 1 week to about 25 years(e.g., 3 months, 6 months, 1 year, 5 years, and 10 years). In otherembodiments, the treatment using one of the methods disclosed hereinoccurs over time and is a chronic treatment.

In some embodiments, the method of treatment, reduces or treats one ormore symptoms of the mitochondrial disease. For example, symptoms maysinclude loss of motor control (e.g., ataxia (abnormal musclecoordination), dystrophic posturing, involuntary movements, andmyoclonus), muscle weakness and pain (e.g., dystonia, hypotonia,lethargy, and myopathy), gastro-intestinal disorders and swallowingdifficulties, poor growth, cardiac disease, liver disease, diabetes,respiratory complications (e.g., respiratory failure), seizures,dementia, coma, visual problems (e.g., eye muscle paralysis, nystagmus,ophthalmoplegia, optic atrophy, and pigmentary retinopathy (retinalcolor changes with loss of vision)), hearing problems (e.g., hearingloss), sensory neuropathy (nerve damage involving the sense organs),lactic acidosis, developmental delays and susceptibility to infection.

In other embodiments, mitochondrial disease causes cell injury or celldeath of cells in the brain, heart, liver, skeletal muscles, kidneys,endocrine system, and respiratory system.

In some embodiments, a mitochondrial disorder involves a deficiency inone or more respiratory chain complexes including Complex I(NADH-coenzyme Q reductase or NADH dehydrogenase), Complex II(succinate-coenzyme Q reductase or succinate dehydrogenase), Complex III(cytochrome bci complex or ubiquinone-cytochrome C oxidoreductase),Complex IV (cytochrome C oxidase), and Complex V (ATP synthase). Inother embodiments, a mitochondrial disorder involves one or more of thefollowing diseases myopathy (muscle disease), mitochondrialencephalomyopathy (brain and muscle disease), fatal infantilemultisystem disorder.

In some embodiments, a mitochondrial disorder is characterized by amutation in a gene selected from the group consisting of AARS2, AASS,ABAT, ABCB6, ABCB7, ABCD1, ACACA, ACAD8, ACAD9, ACADM, ACADS, ACADSB,ACADVL, ACAT1, ACO2, ACSF3, ACSL4, ADCK3, ADCK4, AFG3L2, AGK, AGXT,AIFM1, AK2, ALAS2, ALDH18A1, ALDH2, ALDH3A2, ALDH4A1, ALDH5A1, ALDH6A1,ALDH7A1, AMACR, AMT, APOPT1, ATIC, ATP5A1, ATP5E, ATP6, ATP8, ATPAF2,ATXN2, AUH, BAX, BCKDHA, BCKDHB, BCKDK, BCS1L, BOLA3, C10orf2, C12orf65,CASA, CARS2, CASP8, CAT, CEP89, CHCHD10, CISD2, CLPB, CLPP, COA5, COA6,COASY, COQ2, COQ4, COQ6, COQ9, COX1, COX10, COX14, COX15, COX2, COX20,COX3, COX412, COX6A1, COX6B1, COX7B, CPDX, CPS1, CPT1A, CPT2, CYB5A,CYB5R3, CYC1, CYCS, CYP11A1, CYP11B2, CYP24A1, CYP27A1, CYP27B1, CYTB,D2HGDH, DARS2, DBT, DGUOK, DHCR24, DHODH, DHTKD1, DIABLO, DLAT, DLD,DMGDH, DMPK, DNA2, DNAJC19, DNM1L, EARS2, ECHS1, ELAC2, ETFA, ETFB,ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FECH, FH, FKBP10, FOXRED1, FXN,GARS, GATM, GCDH, GCSH, GDAP1, GFER, GFM1, GK, GLDC, GLRX5, GLUD1,GLYCTK, GPI, GPX1, GRHPR, GTPBP3, HADH, HADHA, HADHB, HARS2, HCCS,HIBCH, HK1, HMBS, HMGCL, HMGCS2, HOGA1, HSD17B10, HSD17B4, HSPD1, HTRA2,IDH2, IDH3B, ISCA2, ISCU, IVD, KARS, KIF1B, KRT5, L2HGDH, LARS2, LIAS,LONP1, LRPPRC, LYRM4, LYRM7, MAOA, MARS2, MCCC1, MCCC2, MCEE, MFN2,MGME1, MICU1, MLH1, MLYCD, MMAB, MMACHC, MMADHC, MOCS1, MPC1, MPV17,MRPL12, MRPL3, MRPL44, MRPS16, MRPS22, mt-12S rRNA, mt-tRNATyr,mt-tRNATrp, mt-tRNAVal, mt-tRNAThr, mt-tRNASer1, mt-tRNASer2,mt-tRNAArg, mt-tRNAG1n, mt-tRNAPro, mt-tRNAAsn, mt-tRNAMet, mt-tRNALeu1,mt-tRNALeu2, mt-tRNALys, mt-tRNAIle, mt-tRNAHis, mt-tRNAGly, mt-tRNAPhe,mt-tRNAGlu, mt-tRNAAsp, mt-tRNACys, mt-tRNAAla, MTFMT, MTO1, MTPAP, MUT,MUTYH, NAGS, NARS2, NCOA4, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA1,NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2,NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB11, NDUFB3, NDUFB9, NDUFS1,NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1,NNT, NUBPL, OAT, OGDH, OGG1, OPA1, OPA3, OTC, OXCT1, PAM16, PANK2,PARK7, PARS2, PC, PCCA, PCCB, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1,PDSS2, PET100, PEX11B, PEX6, PHYH, PINK1, PNPO, PNPT1, POLG, POLG2,PPM1K, PPDX, PRODH, PTRH2, PTS, PUS1, PYCR1, QDPR, RARS, RARS2, RMND1,RPL35A, RPS14, RRM2B, SARS2, SCO1, SCO2, SCP2, SDHA, SDHAF1, SDHAF2,SDHB, SDHC, SDHD, SECISBP2, SERAC1, SFXN4, SLC16A1, SLC19A3, SLC25A1,SLC25A12, SLC25A13, SLC25A15, SLC25A19, SLC25A20, SLC25A22, SLC25A3,SLC25A38, SLC25A4, SNAP29, SOD1, SPG7, SPR, SPTLC2, STAR, SUCLA2,SUCLG1, SUOX, SURF1, TACO1, TARS2, TAZ, TCIRG1, TIMM8A, TK2, TMEM126A,TMEM70, TMLHE, TPI1, TRIT1, TRMU, TRNT1, TSFM, TTC19, TUBB3, TUFM, TYMP,UNG, UQCR10, UQCRB, UQCRC2, UQCRQ, VARS2, WDR81, WFS1, XPNPEP3, andYARS2. In some embodiments, a subject has been identified as having agenetic mutation associated with onset of a mitochondrial disorder(e.g., a mutation in one of the genes identified above) and treatment isinitiated before the onset of symptoms of the disorder.

In some embodiments, a mitochondrial disorder is characterized by apoint mutation in the mitochondrial DNA (mtDNA), deletion within themtDNA, duplication within the mtDNA, or depletion of the mtDNA.

In some embodiments, a mitochondrial disorder is Kearns-Sayre syndrome(KSS), Leber's hereditary optic neuropathy (LHON), myoclonic epilepsyragged red fiber syndrome (MERRF), mitochondrial encephalopathy, lacticacidosis, and stroke (MELAS) syndrome, sensory ataxic neuropathy,dysarthria, and ophthalmoparesis (SANDO) syndrome, maternally inheritedLeigh syndrome (MILS), myopathy and external ophthalmoplegia,neuropathy, gastrointestinal encephalopathy (MNGIE) syndrome, Leighsyndrome, maternally inherited diabetes and deafness (MIDD) syndrome,Alpers-Huttenlocher syndrome, Sengers syndrome, mitochondrial myopathy,lactic acidosis and sideroblastic anemia (MLASA), chronic progressiveexternal ophthalmoplegia (CPEO), autosomal dominant progressive externalophthalmoplegia (AdPEO), neuropathy, ataxia, retinitis pigmentosa (NARP)syndrome, GRACILE syndrome, diabetes insipidus, diabetes mellitus, opticatrophy, and deafness (DIDMOAD) syndrome, or Pearson's syndrome.

In some embodiments, a mitochondrial disorder presents with one or moreof gray matter disease, white matter disease, seizures, migraines,ataxia, stroke, stroke-like episodes, deafness, optic neuropathy,peripheral neuropathy, retinopathy, external opthalmoplegia, liverfailure, kidney failure, pancreatic exocrine dysfunction, intestinalpseudoobstruction, anemia, skeletal muscle myopathy, cardiomyopathy,cardiac conduction defects, short stature, hypogonadism, immunedysfunction, or metabolic acidosis.

In some embodiments, the mitochondrial disorder is diagnosed by analgorithm selected from the group consisting of the Bernier criteria(Bernier et al., “Diagnostic criteria for respiratory chain disorders inadults and children,” Neurology, 59(9):1406-11, 2002), the Moravacriteria (Morava et al., “Mitochondrial disease criteria: diagnosticapplications in children,” Neurology, 67(10):1823-6, 2006), andConsensus from the Mitochondrial Medicine Society (Parikh et al.,“Diagnosis and management of mitochondrial disease: a consensusstatement from the Mitochondrial Medicine Society,” Genetics inMedicine, 17(9):689-701, 2015).

In some embodiments, a subject exhibits mitochondrial dysfunctionassociated with aging. The subject can be, e.g., at least 65 years ofage, at least 70 years of age, at least 75 years of age, or at least 80years of age.

In some embodiments, the subject is treated to prevent (completely orpartially) the occurrence of mitochondrial dysfunction associated withaging. The subject can be, e.g., at least 15 years of age, at least 20years of age, at least 25 years of age, at least 30 years of age, atleast 35 years of age, or at least 40 years of age. The subject in theseembodiments need not exhibit mitochondrial dysfunction or other form ofevident disease.

In some embodiments, a subject exhibits mitochondrial dysfunction thatoccurs in response to an environmental insult such as ingestion ofantibiotics (e.g., tetracycline, chloramphenicol, or aminoglycosides),antivirals (e.g., stavudine), pesticides (e.g., rotenone), or licitdrugs (e.g., MPTP) that are toxic to mitochondria.

In some embodiments, a subject has an oxidative stress disorder.Examples of oxidative stress disorders include Parkinson's disease,Alzheimer's disease, amyotrophic lateral sclerosis, Huntington'sdisease, multiple sclerosis, Asperger syndrome, attention deficithyperactivity disorder, diabetes, cardiovascular disease, cancer, Laforadisease, atherosclerosis, heart failure, myocardial infarction, fragileX syndrome, sickle cell disease, lichen planus, vitiligo, and autism.

In some embodiments, a subject has an inflammatory disorder. Examples ofinflammatory disorders include rheumatoid arthritis, psoriaticarthritis, ankylosing spondylitis, inflammatory bowel disease (e.g.,ulcerative colitis and Crohn's disease), psoriasis, inflammatorymyositis, Langerhans-cell histiocytosis, adult respiratory distresssyndrome, Wegener's granulomatosis, vasculitis, cachexia, stomatitis,idiopathic pulmonary fibrosis, dermatomyositis, polymyositis,non-infectious scleritis, chronic sarcoidosis with pulmonaryinvolvement, myelodysplastic syndrome, moderate to severe chronicobstructive pulmonary disease, and giant cell arteritis.

In a further aspect, the current disclosure provides a method ofscreening for a compound that increases the activity of a hypoxiaresponse comprising

a) administering a candidate compound to a first set of one or morecells with a compromised function of the mitochondrial respiratorychain;

b) measuring the growth of the first set of one or more cells; and

c) comparing the growth of the first set of one or more cells to thegrowth of a second set of one or more cells, wherein the second set ofone or more cells also have compromised function of the mitochondrialrespiratory chain, but have not been administered the candidatecompound,

wherein if the growth of the first set of cells is greater than thegrowth of the second set of cells then the candidate compound increasesthe activity of a hypoxia response.

In some embodiments, cell growth is stunted or arrested when respiratorychain complexes are inhibited for most cell lines. In other embodiments,inhibition of one of the following respiratory chain complexes: ComplexI, Complex III, or Complex V stunts cell growth in most cell lines. Incertain embodiments, inhibition of Complex I, Complex III, or Complex Vstops cell growth in a cell line. In still other embodiments, themethods of screening disclosed herein use one or more cells that areHT-29 cells, HEK 293 cells, or K562 cells.

In another embodiment, a compromised function of the mitochondrialrespiratory chain comprises the presence of genetic defects in one ormore respiratory chain complexes, triggering a mitochondrial lesion, oradministering an inhibitor of one or more respiratory chain complexes.In other embodiments, the compromised function of the mitochondrialrespiratory chain comprises an inhibitor of one or more respiratorychain complexes. In still another embodiment, the compromised functionof the mitochondrial respiratory chain comprises administration ofantimycin to the one or more cells in the presence of pyruvate. In yetanother embodiment, the compromised function of the mitochondrialrespiratory chain further comprises the reduction of or removal ofpyruvate.

In other embodiments, cell growth is reduced by administering a ComplexI inhibitor, a Complex III inhibitor, or a Complex V inhibitor. Inanother embodiment, the compromised function of the mitochondrialrespiratory chain comprises an inhibition selected from the groupconsisting of: Complex III Inhibition, Complex I Inhibition, Complex VInhibition, and ATP (adenosine triphosphate) Synthase Inhibition. Instill other embodiments, the compromised function of the mitochondrialrespiratory chain comprises administering a Complex I inhibitor, aComplex III inhibitor, or a Complex V inhibitor. In another embodiment,the Complex I inhibitor is selected from the group consisting ofacetogenins, reduced nicotinamide adenine dinucleotide (NADH) analogs,and metformin. In yet another embodiment, the Complex I inhibitor isselected from the group consisting of annonacin, bullatacin,rolliniastatin-2, uvaricin, adenosine diphosphate ribose, piericidin,rotenone, and metformin. In still another embodiment, the Complex IIIinhibitor is selected from the group consisting of Q_(i) site inhibitorsand Q_(o) site inhibitors. In a further embodiment, the Complex IIIinhibitor is selected from the group consisting of Antimycin,myxothiazol, stigmatellin, and strobilurin derivatives. In someembodiments, the ATP synthase inhibitor is selected from the groupconsisting of oligomycins, α-helical basic peptide inhibitors,catechins, catecholestrogens, flavones, polyketide inhibitors,stilbenes, tentoxin and derivatives, and nucleotide analogs. In someembodiments, the ATP synthase inhibitor is selected from the groupconsisting of oligomycin, melittin, epicatechin, epicatechin gallate,epigallocatechin gallate, 4-hydroxyestradiol, 2-hydroxyestradiol,quercetin, morin, kaempferol, genistein, peliomycin, venturicidin A,venturicidin B, venturicidin X, ossamycin, resveratrol, piceatannol,diethylstilbestrol, tentoxin, GTP, FTP, and TNP-ATP.

In another aspect, the current disclosure provides a method of screeningfor targets for the modulation of mitochondrial respiratory chainfunction by genetic engineering techniques. In one aspect, the geneticengineering technology comprises a recombinant CRISPR-Cas expressionsystem. In one embodiment, the Cas protein is complexed with a sgRNA asprovided herein and in the art. In one embodiment, the method ofscreening for targets for modulation of mitochondrial respiratory chainfunction comprising

a) administering to a first set of one or more cells one or more sgRNAstargeting at least one gene in the human genome;

b) compromising the function of the mitochondrial respiratory chain inthe first set of one or more cells;

c) measuring the relative enrichment of sgRNAs in the first set of oneor more cells; and

d) comparing the corresponding enrichment of sgRNAs of the first set ofone or more cells to the enrichment in a second set of one or morecells, wherein the second set of one or more cells have beenadministered the same one or more sgRNAs, but have less compromisedfunction of the mitochondrial respiratory chain,

wherein if the relative enrichment of a sgRNA in the first set of cellsis greater than the corresponding enrichment in the second set of cellsthen the gene is a target for the modulation of cellular or whole bodyresponse to mitochondrial respiratory chain (dys)function.

In another embodiment, compromising the function of the mitochondrialrespiratory chain comprises introducing genetic defects in one or morerespiratory chain complexes, triggering a mitochondrial lesion, oradministering an inhibitor of one or more respiratory chain complexes.In other embodiments, the compromise of function of the mitochondrialrespiratory chain comprises administration of an inhibitor of one ormore respiratory chain complexes. In still another embodiment, thecompromise of function of the mitochondrial respiratory chain comprisesadministration of antimycin to the one or more cells in the presence ofpyruvate. In yet another embodiment, the compromise of function of themitochondrial respiratory chain further comprises the reduction of orremoval of pyruvate.

In yet another aspect, the current disclosure provides a compositioncomprising a nucleic acid molecule comprising a sequence selected fromthe group consisting of:

(SEQ ID NO: 1) AGTACCTGGCAGTGTGATAT (SEQ ID NO: 2) CAGGTCGCTCTACGAAGATC(SEQ ID NO: 3) CGCGCGTCGTGCTGCCCGTA (SEQ ID NO: 4) GTGCCATCTCTCAATGTTGA(SEQ ID NO: 5) TGTCCGTCAACATTGAGAGAwherein the nucleic acid molecule is functionally integrated with aviral vector.

A physician or veterinarian having ordinary skill in the art can readilydetermine and prescribe the effective amount required by the methods oftreatment. For example, the physician or veterinarian could start dosesof the inhibitors or sequences of the invention employed in the methodsat levels lower than that required in order to achieve the desiredtherapeutic effect and gradually increase the dosage until the desiredeffect is achieved.

It will be understood by those having ordinary skill in the art that thespecific dose level and frequency of dosage for any particular patientor subject may be varied and will depend upon a variety of factorsincluding the efficacy of the specific method employed, the metabolicstability and length of action of that method, the age, body weight,general health, gender, diet, and the severity of the particularmitochondrial disorder being treated. In addition specific dose leveland frequency of dosage for any particular patient also may depend onfactors including, but not limited to, other medications, allergies, andprior experiences with treatments. For example, some patients may betreated using methods of this disclosure over a period of years if themitochondrial disorder is a chronic condition.

In additional embodiments, assay screening kits are provided. The kitincludes a container for the screening assay. An instruction for the useof the assay and the information about the screening method are to beincluded in the kit. In some embodiments, the kit may also contain aComplex I inhibitor, a Complex III inhibitor, or a Complex V inhibitorto mimic a mitochondrial respiratory chain disorder. In otherembodiments, the kit may also contain sgRNAs having a nucleic acidsequence comprising one or more sequences targeting at least one gene inthe human genome.

C. Hypoxia Therapy

Mitochondrial dysfunction, an oxidative stress disorder, or aninflammatory disorder can be treated or prevented by administering to asubject by inhalation a therapeutically effective amount of atherapeutic gas comprising between 5 to 20% O₂. A hypoxia inductionsystem can be used to prepare the therapeutic gas that is administeredto the subject.

In a first example, a hypoxia induction system contains a firstcontainer containing a first gas comprising nitrogen and a secondcontainer containing a second gas comprising oxygen, and theoxygen-depleted air delivered to the subject is prepared by mixing thefirst gas and the second gas.

In a second example, a hypoxia induction system intakes ambient air,reduces the oxygen content of the intake air, to produce theoxygen-depleted air that is delivered to the subject. Colorado AltitudeTraining (CAT) provides a portable enclosure system that produceshypoxic air by this mechanism. CAT uses a high-flow hypoxic air deliveryunit and a semi-sealed enclosure. The air unit draws in ambient room airand separates the oxygen molecules from the nitrogen molecules, creatingthe hypoxic or oxygen reduced air. Simulated altitudes of up to 14,500feet can be achieved, and can be controlled to within 100 feet accuracyusing CAT's digital control system. Hypoxico Altitude Training Systemsdevices generate hypoxic air in a manner similar to the CAT system.Simulated altitudes of about 21,500 feet can be achieved with theHypoxico Altitude Training Systems.

In a third example, a hypoxia induction system intakes ambient air, addsnitrogen to the intake air, to produce the oxygen-depleted air that isdelivered to the subject. The nitrogen can provided from, e.g., liquidnitrogen, cylinders of highly purified nitrogen (e.g., 100% nitrogen),or cylinders containing nitrogen (e.g., 80-95%) and oxygen (e.g.,5-20%). Nitrogen used to produce oxygen-depleted air can optionally beproduced by pressure swing adsorption (PSA). Under high pressure, gasestend to be adsorbed to solid surfaces. When the pressure is reduced, thegas is desorbed. If air is passed under pressure through a vesselcontaining a carbon molecular sieve, oxygen gas is adsorbed and gasenriched in nitrogen and depleted in oxygen is produced. Dual step PSAcan be used to produce a highly pure nitrogen gas: first, compressed airis forced through a carbon molecular sieve to produce nitrogen at apurity of approximately 98%; second, the nitrogen produced in the firststep is forced into a second carbon molecular sieve and the nitrogen gasreaches a purity up to 99.999%. This nitrogen gas can be combined withambient air to produce oxygen-depleted air that is delivered to thesubject. Alternatively, if air is passed under pressure through a vesselcontaining an adsorbent bed of zeolite that attracts nitrogen morestrongly than it does oxygen, part or all of the nitrogen will stay inthe bed. When the bed reaches the end of its capacity to adsorbnitrogen, the pressure can be reduced to release the adsorbed nitrogen.This released nitrogen can be combined with ambient air to produceoxygen-depleted air that is delivered to the subject.

The therapeutic gas delivered to the subject can contain between 5 to20% O₂. The proportion of oxygen in the therapeutic gas can vary basedupon factors including the age of the subject, the condition treated,and the duration of the hypoxic treatment. For example, the therapeuticgas can contain between 5 to 20% O₂, between 6 to 18% O₂, between 7 to17% O₂, between 8 to 16% O₂, between 9 to 15% O₂, between 10 to 15% O₂,between 10 to 14% O₂, between 10 to 13% O₂, between 10 to 12% O₂, orbetween 10 to 11% O₂. In some embodiments, the therapeutic gas containsabout 5% O₂, about 6% O₂, about 7% O₂, about 8% O₂, about 9% 02, about10% O₂, about 11% O₂, about 12% O₂, about 13% O₂, about 14% O₂, about15% O₂, about 16% O₂, about 17% O₂, or about 18% O₂.

The therapeutic gas can be administered to the subject by devicesincluding but not limited to nasal prongs, a face mask, an enclosed tentor chamber (completely or semi-sealed), an intra-tracheal catheter, anendotracheal tube, or a tracheostomy tube. The use of nasal prongs or aface mask allow for greater mobility of the subject while being treatedwith the therapeutic gas.

The therapeutic gas can optionally be inhaled by the subjectcontinuously over the course of a variety of time periods (e.g., atleast 1 minute, at least 2 minutes, at least 3 minutes, at least 4minutes, at least 5 minutes, at least 6 minutes, at least 7 minutes, atleast 8 minutes, at least 9 minutes, at least 10 minutes, at least 15minutes, at least 1 hour, at least 2 hours, at least 4 hours, at least 8hours, at least 12 hours, at least 24 hours, at least 48 hours, orlonger). In some instances, administration of the therapeutic gas isintermittent (e.g., only during inspiration to save gas (sensinginspiration by a variety of methods, temperature, pressure, etc.)) oronly for a few hours each day, wherein the therapeutic gas is inhaled(e.g., for a period of time specified above), followed by breathingambient air, which is then followed by one or more additional periods ofbreathing the therapeutic gas.

The therapeutic gas can optionally be administered to a subject duringsleep. This can be achieved by, for example, positioning a tent over abed or placing a bed within an enclosed chamber. For children orinfants, a tent can be positioned over a crib or a crib can be placedwithin an enclosed chamber.

A subject treated with the therapeutic gas can be monitored to measurethe effects mediated by the treatment. For example, arterial oxygensaturation (SpO₂) can be measured in the subject one or more times(continuously or intermittently) after administration of the therapeuticgas to the subject. The measured SpO₂ value can be used to feedback andadjust (e.g. automatically adjust) the oxygen content of theadministered therapeutic gas so as to maintain SpO₂ in the subject inthe range of 50-90% (e.g., 60-90%, 70-90%, 75-90%, 80-90%, 85-90%, orabout 85%). In addition or alternatively, arterial partial oxygenpressure (PaO₂) can be measured in the subject one or more times(continuously or intermittently) after administration of the therapeuticgas to the subject. The measured PaO₂ value can be used to feedback andadjust (e.g. automatically adjust) the oxygen content of theadministered therapeutic gas so as to maintain PaO₂ in the subject inthe range of 25 mm Hg to 90 mm Hg (e.g., 25 mm Hg to 70 mm Hg, 25 mm Hgto 60 mm Hg, 25 mm Hg to 55 mm Hg, 25 mm Hg to 45 mm Hg, 25 mm Hg to 40mm Hg, 25 mm Hg to 35 mm Hg, 35 mm Hg to 70 mm Hg, 35 mm Hg to 60 mm Hg,45 mm Hg to 60 mm Hg, 50 mm Hg to 60 mm Hg, 55 mm Hg to 60 mm Hg, orabout 55 mm Hg). In some embodiments, SpO₂ and PaO₂ are both measured inthe subject one or more times (continuously or intermittently) afteradministration of the therapeutic gas to the subject. The measured SpO₂and PaO₂ values can be used to feedback and adjust (e.g. automaticallyadjust) the oxygen content of the administered therapeutic gas so as tomaintain SpO₂ and PaO₂ in the subject in the range of 50-90% SpO₂ and 25mm Hg to 70 mm Hg PaO₂ (e.g., 80-90% SpO₂ and 50 mm Hg to 60 mm Hg PaO₂,85-90% SpO₂ and 55 mm Hg to 60 mm Hg PaO₂, or about 85% SpO₂ and about55 mm Hg PaO₂).

Blood hematocrit and/or circulating hemoglobin levels can be measured ina subject one or more times after administration of the therapeutic gasto the subject, wherein the detection of an increase in blood hematocritand/or an increase in circulating hemoglobin levels after initiation ofthe treatment indicates that the treatment is having its desired effect.A decision of whether or how to continue the treatment can be based uponthe measured blood hematocrit and/or circulating hemoglobin levels. Forexample, if the measured blood hematocrit and/or circulating hemoglobinlevels exceed a pre-established target level, then the treatment may beterminated or the oxygen content of the administered therapeutic gas maybe increased. In another example, if the measured blood hematocritand/or circulating hemoglobin levels are below a pre-established targetlevel, then the duration of the treatment may be extended and/or theoxygen content of the therapeutic gas may be decreased.

A system for treatment or prevention according to the methods describedherein can optionally contain: (i) an enclosed tent or chamber or abreathing apparatus; (ii) a hypoxia induction system that deliversoxygen-depleted air to the enclosed tent or chamber or the breathingapparatus, wherein the oxygen-depleted air comprises between 5 to 20% O₂(or any of the oxygen concentrations described herein); and (iii) adevice (such as a pulse oximeter) that measures SpO₂ in a subjectbreathing air within the enclosed tent or chamber or from the breathingapparatus, wherein the system adjusts the oxygen content of theoxygen-depleted air delivered to the enclosed tent or chamber or thebreathing apparatus based upon the SpO₂ measured by the device such thatSpO₂ in the subject is maintained within the range of 50% to 90% (or anyof the SpO₂ target ranges or values described herein).

A system for treatment or prevention according to the methods describedherein can optionally contain: (i) an enclosed tent or chamber or abreathing apparatus; (ii) a hypoxia induction system that deliversoxygen-depleted air to the enclosed tent or chamber or the breathingapparatus, wherein the oxygen-depleted air comprises between 5 to 20% O₂(or any of the oxygen concentrations described herein); and (iii) adevice that measures PaO₂ in a subject breathing air within the enclosedtent or chamber or from the breathing apparatus, wherein the systemadjusts the oxygen content of the oxygen-depleted air delivered to theenclosed tent or chamber or the breathing apparatus based upon the PaO₂measured by the device such that PaO₂ in the subject is maintainedwithin the range of 25 mm Hg to 90 mm Hg (or any of the PaO₂ targetranges or values described herein).

Mitochondrial dysfunction, an oxidative stress disorder, or aninflammatory disorder can also be treated or prevented by causing asubject to breathe a therapeutically effective amount of air in ahypobaric chamber. In some instances, the hypobaric chamber has anatmospheric pressure equivalent to that between 1,500 meters to 10,000meters above sea level (e.g., equivalent to 1,500 meters to 10,000meters above sea level, equivalent to 2,000 meters to 8,000 meters abovesea level, equivalent to 2,000 meters to 7,000 meters above sea level,equivalent to 2,000 meters to 6,000 meters above sea level, equivalentto 2,000 meters to 5,000 meters above sea level, equivalent to 2,000meters to 4,000 meters above sea level, equivalent to 2,000 meters to3,000 meters above sea level, equivalent to 2,000 meters to 2,500 metersabove sea level, equivalent to 3,000 meters to 7,000 meters above sealevel, equivalent to 3,000 meters to 6,000 meters above sea level,equivalent to 3,000 meters to 5,000 meters above sea level, equivalentto 3,000 meters to 4,000 meters above sea level, equivalent to 4,000meters to 7,000 meters above sea level, equivalent to 4,000 meters to6,000 meters above sea level, equivalent to 4,000 meters to 5,000 metersabove sea level, equivalent to 5,000 meters to 8,000 meters above sealevel, equivalent to 5,000 meters to 7,000 meters above sea level,equivalent to 5,000 meters to 6,000 meters above sea level, equivalentto 6,000 meters to 8,000 meters above sea level, equivalent to 6,000meters to 7,000 meters above sea level, or equivalent to 7,000 meters to8,000 meters above sea level).

In some subjects, such as some children or newborns, hypoxic breathingaccording to a method described herein may have adverse effects, such ascausing pulmonary vasoconstriction, pulmonary hypertension, or shuntingvia the ductus arteriosus or a patent foramen ovale. To assist indilating the pulmonary circulation and avoiding, or reducing theoccurrence of, or alleviating potential adverse effects of hypoxicbreathing, gaseous nitric oxide can optionally be administered to asubject in combination with breathing a therapeutic gas or breathing airin a hypobaric chamber to produce systemic hypoxia according to a methodof treatment or prevention described herein. See Frostell et al. (1993)Anesthesiology 78:427-35. In embodiments where a subject is administereda therapeutic gas with reduced oxygen content, nitric oxide canoptionally be administered within the therapeutic gas having reducedoxygen content. In some embodiments, lower body SpO₂ (e.g., toe) ismeasured in a subject (e.g., a child or infant) and nitric oxide isadded to the inhaled therapeutic gas in an amount that causes the lowerbody SpO₂ to increase so as to decrease or eliminate the differencebetween lower body SpO₂ and upper body SpO₂ (e.g., as measured in afinger or ear).

Methods for safe and effective administration of nitric oxide aredescribed in, e.g., Zapol, U.S. Pat. No. 5,570,683; Zapol et al., U.S.Pat. No. 5,904,938; Bach et al., U.S. Published Application No.20030039638; Higenbottam, U.S. Pat. No. 5,839,433; and Frostell et al.(1991) Circulation 83:2038. Pharmaceutical grade nitric oxide forinhalation is available commercially (INOmax™, MallinckrodtPharmaceuticals).

The concentration of gaseous nitric oxide in the therapeutic gasadministered to the subject can be, for example, at least 5 ppm, atleast 10 ppm, at least 20 ppm, at least 40 ppm, at least 50 ppm, atleast 80 ppm, at least 100 ppm, at least 200 ppm, at least 300 ppm, orat least 500 ppm. In some embodiments, the concentration of gaseousnitric oxide in the therapeutic gas is in the range of 0.5 ppm to 500ppm (e.g., 0.5 ppm to 200 ppm, 0.5 ppm to 80 ppm, 1 ppm to 200 ppm, 1ppm to 100 ppm, 1 ppm to 50 ppm, or 5 ppm to 40 ppm).

Gaseous nitric oxide can be administered by inhalation from a source ofstored, compressed nitric oxide gas. The source of nitric oxide can be100% nitric oxide, or diluted with N₂ or any other inert gas (e.g.,helium). The nitric oxide can be obtained and stored as a mixture freeof any contaminating 02 or higher oxides of nitrogen, because suchhigher oxides of nitrogen (which can form by reaction of 02 with nitricoxide) are potentially harmful to lung tissues. If desired, purity ofthe nitric oxide may be demonstrated with chemiluminescence analysis,prior to administration to a patient. Chemiluminescence NO—NO_(x)analyzers are commercially available (e.g., Model 14A, ThermoEnvironmental Instruments, Franklin, Mass.). The NO—N₂ mixture may beblended with O₂ or an O₂-containing gas such as air through, forexample, calibrated rotameters which have been validated previously witha spirometer. The final concentration of nitric oxide in the breathingmixture may be verified with a chemical or chemiluminescence technique(see, e.g., Fontijin et al., Anal. Chem. 42:575 (1970)). Nitric oxidegas may also be mixed with room air, using a standard low-flow blender(e.g., Bird Blender, Palm Springs, Calif.). Nitric oxide may begenerated from a mixture of N₂ and O₂ (i.e., air) by using an electricplasma nitric oxide generator. Such a generator is described in Zapol,U.S. Pat. No. 5,396,882 and US published application number 20160030699.

Xenon upregulates hypoxia inducible factor 1 alpha and can be used totreat mitochondrial dysfunction, an oxidative stress disorder, or aninflammatory disorder according to the methods described herein. In someembodiments xenon can be administered to a subject in combination withbreathing a reduced oxygen content therapeutic gas or breathing air in ahypobaric chamber according to a method of treatment or preventiondescribed herein. In embodiments where a subject is administered atherapeutic gas with reduced oxygen content, xenon can optionally beadministered within the therapeutic gas. The concentration of xenon (ananesthetic gas with therapeutic properties in ischemia-reperfusion) inthe therapeutic gas administered to the subject can be, for example,20-70% (e.g., 30-60%, 30-50%, 40-50%, 40-50%, about 40%, or about 45%).

D. Pharmaceutical Compositions

As used herein the term “pharmaceutical composition” refers to apreparation of one or more of the components described herein, orphysiologically acceptable salts or prodrugs thereof, with otherchemical components such as physiologically suitable carriers andexcipients. The purpose of a pharmaceutical composition is to facilitateadministration of a compound to an organism. The term “prodrug” refers aprecursor compound that can hydrolyze, oxidize, or otherwise react underbiological conditions (in vitro or in vivo) to provide the activecompound.

The term “excipient” refers to an inert or inactive substance added to apharmaceutical composition to further facilitate administration of acompound. Non-limiting examples of excipients include calcium carbonate,calcium phosphate, various sugars and types of starch, cellulosederivatives, gelatin, vegetable oils and polyethylene glycols.

The pharmaceutical compositions of the present invention PHD inhibitorsselected from the group consisting of 2-oxoglutarate analogs (also knownas α-ketoglutarate), β-oxocarboxylic acids, and BAY-85-3934. In someembodiments, the PHD inhibitor is FG-4592 or roxadustat. Pharmaceuticalcompositions can be formulated into a single dosage form. In certainembodiments, this dosage form is an oral dosage form. This oral dosageform can be in the form of tablets, pills, dragees, capsules, liquids(aqueous or non-aqueous solutions), gels, syrups, slurries, gelcaps,lozenges, suspensions, and the like, for oral ingestion by a patient. Incertain embodiments, one or more of the pharmaceutical compositions arein a slow release composition or have been formulated to affect releasefrom the oral dosage form. In other embodiments, these dosage forms canbe administered by any method known in the art including intravenouslyand intraperitoneally.

The pharmaceutical compositions of the present invention may bemanufactured by processes well known in the art, e.g., by means ofconventional mixing, dissolving, granulating, grinding, pulverizing,dragee-making, levigating, emulsifying, encapsulating, entrapping or bylyophilizing processes.

The compositions for use in accordance with the present invention thusmay be formulated in conventional manner using one or morepharmaceutically acceptable carriers comprising excipients andauxiliaries, which facilitate processing of the active compounds intopreparations which can be used pharmaceutically. Proper formulation isdependent upon the route of administration chosen.

The term “administration” or any lingual variation thereof as usedherein is meant any way of administration. The pharmaceuticalcomposition may be administered in one therapeutic dosage form or in twoseparate therapeutic dosages such as in separate capsules, tablets orinjections. In the case of the two separate therapeutic dosages, theadministration may be such that the periods between the administrationsvary or are determined by the practitioner. It is however preferred thatthe second drug is administered within the therapeutic response time ofthe first drug. The multiple therapeutic dosage forms may beadministered either at the same time, or separately, or sequentially,according to the invention, do not represent a mere aggregate of knownagents, but a new combination with the valuable property that theeffectiveness of the treatment is achieved at a much lower dosage ofsaid at least one additional drug.

The pharmaceutical compositions of the present invention may beadministered by any convenient route, for example, by infusion or bolusinjection, by absorption through epithelial or mucocutaneous linings(e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may beadministered together with any other therapeutic agent. Administrationcan be systemic or local.

Various delivery systems are known, e.g., encapsulation in liposomes,microparticles, microcapsules or capsules that may be used to administerthe compositions of the invention. Methods of administration include butare not limited to intradermal, intramuscular, intraperitoneal,intravenous, subcutaneous, intranasal, epidural, oral, sublingual,intranasal, intracerebral, intravaginal, transdermal, rectally, byinhalation, or topically to the cars, nose, eyes, or skin. The preferredmode of administration is left to the discretion of the practitioner,and will depend in part upon the site of the medical condition (such asthe site of cancer) and the severity of thereof.

For example, for injection the composition of the invention may beformulated in aqueous solutions, preferably in physiologicallycompatible buffers such as Hank's solution, Ringer's solution, orphysiological saline buffer. For transmucosal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants for example DMSO, or polyethylene glycol are generallyknown in the art.

For oral administration, the composition can be formulated readily bycombining the active components with any pharmaceutically acceptablecarriers known in the art. Such “carriers” may facilitate themanufacture of such as tablets, pills, dragees, capsules, liquids, gels,syrups, slurries, suspensions, and the like, for oral ingestion by apatient. Pharmacological preparations for oral use can be made using asolid excipient, optionally grinding the resulting mixture, andprocessing the mixture of granules, after adding suitable auxiliaries ifdesired, to obtain tablets or dragee cores. Suitable excipients are, inparticular, fillers such as sugars, including lactose, sucrose,mannitol, or sorbitol; cellulose preparations such as, for example,maize starch, wheat starch, rice starch, potato starch, gelatin, gum,methyl cellulose, hydroxypropylmethyl-cellulose, sodiumcarbomethylcellulose, and/or physiologically acceptable polymers such aspolyvinylpyrrolidone (PVP). If desired, disintegrating agents may beadded, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acidor a salt thereof such as sodium alginate.

Dragee cores are provided with suitable coatings. For this purpose,concentrated sugar solutions may be used which may optionally containgum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethyleneglycol, titanium dioxide, lacquer solutions and suitable organicsolvents or solvent mixtures.

Pharmaceutical compositions, which can be used orally, include push-fitcapsules made of gelatin as well as soft, sealed capsules made ofgelatin and a plasticizer, such as glycerol or sorbitol. The push-fitcapsules may contain the active ingredients in admixture with fillersuch as lactose, binders such as starches, lubricants such as talc ormagnesium stearate and, optionally, stabilizers. In soft capsules, theactive components may be dissolved or suspended in suitable liquids,such as fatty oils, liquid paraffin, or liquid polyethylene glycols.

Dyestuffs or pigments may be added to the tablets or dragee coatings foridentification or to characterize different dosages or dosage forms. Inaddition, stabilizers may be added.

Pharmaceutical compositions for parenteral administration includeaqueous solutions of the active preparation in a water-soluble form.Additionally, suspensions of the active preparation may be prepared asoily injection suspensions. Suitable lipophilic solvents or vehiclesinclude fatty oils such as sesame oil, or synthetic fatty acids esterssuch as ethyl oleate, triglycerides or liposomes. Aqueous injectionsuspensions may contain substances, which increase the viscosity of thesuspension, such as sodium carboxymethyl, cellulose, sorbitol ordextran. Optionally, the suspension may also contain suitablestabilizers or agents, which increase the solubility of the compounds,to allow for the preparation of highly concentrated solutions.

Alternatively, the composition may be in a powder form for constitutionbefore use with a suitable vehicle, e.g., sterile, pyrogen-free water.The exact formulation, route of administration and dosage may be chosenby the physician familiar with the patient's condition. (See for exampleFingl, et al., 1975, in “The Pharmacological Basis of Therapeutics”,Chapter I, p. 1). Depending on the severity and responsiveness of thecondition treated, dosing can also be a single administration of a slowrelease composition, with course of treatment lasting from several daysto several weeks or until cure is effected or diminution of the diseasestate is achieved.

The following examples are provided to further elucidate the advantagesand features of the present application, but are not intended to limitthe scope of the application. The examples are for the illustrativepurposes only.

EXAMPLES Example 1: Mitochondrial Disease Model

Mitochondrial disease was modeled in the suspension cell line, K562, anda CRISPR screen was performed to identify potential drug targets. Thenatural product, Antimycin, was used as a complex III inhibitor of therespiratory chain. In the presence of Antimycin, the respiratory chainis unable to oxidize high energy reducing equivalents to power ATPproduction. However, redox recycling by the cytoplasmic lactatedehydrogenase reaction, allows other NAD+ dependent reactions toproceed. Removal of pyruvate in the presence of respiratory chaininhibition resulted in reductive stress, further preventing cellproliferation (King, Science, 246:500-03 (1989)). Mitochondrial diseasewas modeled with the addition of Antimycin alone (moderate disease) orAntimycin in combination with removal of pyruvate (severe disease),using cell growth as a proxy for disease magnitude (FIG. 3). K562 cellswere infected with a 65,000 sgRNA library, targeting ˜18,000 genes(Shalem et al., Science, 343:84-88 (2014)). After one week of genomeediting, the pool of knockout cells were divided into experimentalconditions of untreated, moderate disease and severe disease states(FIG. 4). Samples for an enrichment screen were collected by allowingthe knockout pool to grow in selection conditions for three weeks. Therelative growth between untreated and moderate disease conditions was100-fold and between untreated and severe disease conditions was10,000-fold (FIG. 5).

Three weeks of genome editing in untreated cells led to a significantdepletion of sgRNAs corresponding to essential genes, including thoserelated to transcription, translation, and splicing. Nearly 20% of the500 most essential genes were mitochondrial proteins, especiallymitochondrial ribosomal proteins and electron transport chain subunits(Table 1). As mitochondrial proteins make up approximately 5% of theproteome, this enrichment highlighted the dramatic effects ofmitochondrial dysfunction on viability. Lesions in such essentialmitochondrial genes are likely to be disease-causing.

TABLE 1 Examples of essential mitochondrial protein genes HGNC symbolEntrezGene ID MitoCarta ABHD11 83451 1 ACSM2A 123876 1 AIFM1 9131 1ATP5I 521 1 ATP5J2 9551 1 ATPAF2 91647 1 BCS1L 617 1 CARS2 79587 1 CLPP8192 1 COX15 1355 1 COX6C 1345 1 CTU1 90353 1 CYB5B 80777 1 DAP3 7818 1DARS2 55157 1 DNAJA3 9093 1 DNAJC11 55735 1 FDXR 2232 1 FH 2271 1 FPGS2356 1 GADD45GIP1 90480 1 GFM1 85476 1 GLRX5 51218 1 GRPEL1 80273 1 HSCB150274 1 HSD17B10 3028 1 ISCA2 122961 1 LETM1 3954 1 LIPT1 51601 1 LIPT2387787 1 LYRM4 57128 1 METTL17 64745 1 MRPL12 6182 1 MRPL13 28998 1MRPL16 54948 1 MRPL17 63875 1 MRPL20 55052 1 MRPL28 10573 1 MRPL47 571291 MRPL49 740 1 MRPL53 116540 1 MRPS18A 55168 1 MRPS18B 28973 1 MRPS2464951 1 MRPS25 64432 1 MRPS28 28957 1 MRPS34 65993 1 MRPS35 60488 1MRPS7 51081 1 MTCH2 23788 1 MTHFD2 10797 1 MTIF3 219402 1 NDUFA2 4695 1NDUFAF3 25915 1 NDUFAF5 79133 1 NDUFB10 4716 1 NDUFB4 4710 1 NDUFB9 47151 NDUFS2 4720 1 NNT 23530 1 NUBPL 80224 1 PARS2 25973 1 PDSS2 57107 1PGS1 9489 1 PHB 5245 1 PHB2 11331 1 PNPT1 87178 1 POLG2 11232 1 PPA227068 1 RFK 55312 1 ROMO1 140823 1 RPL35A 6165 1 RPS15A 6210 1 SDHA 63891 SDHB 6390 1 SHMT2 6472 1 SLC16A1 6566 1 SLC25A26 115286 1 SOD2 6648 1SUPV3L1 6832 1 TFB2M 64216 1 TIMM44 10469 1 TIMMDC1 51300 1 TOMM22 569931 TXN2 25828 1 VARS2 57176 1 YARS2 51067 1

Out of the approximately 18,000 genes tested, the CRISPR screenidentified the inhibition of Von Hippel Lindau (VHL) factor as the mosteffective genetic suppressor for mitochondrial disease, in both themoderate and severe disease conditions. RNAi Gene Enrichment Ranking(RIGER) analysis ranked VHL knockout cells as the most enriched overtime in both infection replicates corresponding to severe and moderatedisease. For example, the five sgRNAs spanning all three exons of VHLranked 1, 2, 3, 12 and 14 out of approximately 65,000 total guides forenrichment in disease conditions relative to pre-treatment conditions(Table 2 and FIGS. 6-9). Furthermore, the most significant VHL sgRNAswere enriched greater than 20-fold in disease states (FIG. 10). Even thesecond-ranked gene target was appreciably less enriched relative to VHL,reflecting the limited therapeutic targets available for mitochondrialrespiratory chain dysfunction. Of note, VHL knockout cells were alsoenriched in untreated conditions over time, reflecting an overall effecton cell growth. However, this enrichment was significantly less than indisease conditions.

TABLE 2 Enrichment of sgRNAs and corresponding genes based on CRISPR indisease conditions relative to pre-treatment conditions. Gene CRISPRGuide Ranks Rank VHL 1, 2, 3, 12, 14 1 RGS20 13, 145, 2266, 8296, 27675,29239 2 SIN3A 32, 242 3 ESPNL 168, 199, 8244, 8519, 12532, 58512 4EXOC3L4 47, 267, 6259, 7589 5 DOCK7 177, 299, 4796, 10550, 18350, 236446 NDUFS6 8, 403, 2876, 7677 7 CLSTN1 7, 412, 11644, 46491 8 CD101 139,372, 14840, 30593, 57365, 61388 9 TRIO 277, 342, 1831, 23700, 37855 10

VHL activity is a key regulator of the hypoxia response pathway (Ohh etal., Nature Cell Biol. 2:423-27 (2000)). Organisms have evolvedelaborate defense mechanisms to cope with changing oxygen tensions andextreme environments. In normoxic conditions, the hypoxia inducibletranscription factors (HIF) are constitutively made and hydroxylated bythe prolyl-hydroxylase (PHD) enzymes (FIG. 1) (Majmunder et al.,Molecular Cell. 40:294-309 (2010)). The hydroxylated form is recognizedby the ubiquitin ligase, VHL, and targeted for degradation. Duringhypoxia, the PHD reaction does not take place, allowing HIF1αstabilization and activation of the hypoxia transcriptional program.VHL-knockout cells show HIF1α stabilization, even during normoxicconditions, thereby bypassing cellular oxygen sensing mechanisms (Ivanet al., Proc. Natl. Acad. Sci. U.S.A. 99:13459-64 (2002)).

VHL was validated and characterized as a therapeutic target by testingthe ability of VHL-knockout cells to withstand respiratory chaindysfunction. VHL-modified cells showed increased cell proliferation inthe presence of Antimycin (moderate and severe disease conditions)relative to non-targeting (dummy) sgRNA-modified cells (FIG. 11).Furthermore, there was a strong positive correlation between the degreeof VHL sgRNA enrichment in the CRISPR screen and the rescue effect sizeof individual sgRNAs, likely reflecting differences in genome editingefficiencies. The therapeutic value in the context of complex IIIdeficiency could be extended to lesions in other mitochondrialcomplexes. VHL-knockout cells were also more resistant to Complex Iinhibition by Piericidin and ATP synthase inhibition by Oligomycin,demonstrating the broad utility of this therapeutic approach. Asmitochondrial disease encompasses such a diverse set of genetic lesionsimpacting the respiratory chain complexes in varying combinations, sucha generic therapeutic is especially attractive. A genome-wide CRISPRscreen identified the hypoxia response pathway as the strongestsuppressor of mitochondrial disease.

Example 2: Genome-Wide CRISPR Screen

Virus Production

The genome-scale CRISPR knockout (GECKO) library vl was generouslyprovided by the Zhang Lab. Library details have previously beenpublished (Shalem et al., Science, 343:84-88 (2014)). For librarylentivirus production, 1.2e7 cells were placed in each of 25, T225flasks in 50 ml of full DMEM (Life Technologies 11995) media (containingPen/Strep, 10% FBS). 18 h later, media in each flask was replaced with13 ml of DMEM (no Pen/Strep, 10% FBS) and 2 h later, media was replacedwith 20 ml OptiMEM (Life Technologies 31985-070; no serum, noPen/Strep). A transfection mastermix was made by combining individuallyprepared mastermix A (94 ml of OptiMEM, 2.4 ml of Lipofectamine 2000(Life Technologies)) and mastermix B (94 ml OptiMEM, 2.1 ml of PLUSReagent (Life Technologies), 240 μg of pVSVg plasmid, 360 μg of psPAX2plasmid and 480 μg of GECKO plasmid library). Mastermixes A and B werecombined at RT for 20 m. 8 ml of the final mastermix was added to eachT225 flask of HEK 293 cells. After 6 h, the media was changed to 30 mlof DMEM media (w/1% BSA (Sigma)) and cells were incubated for 48-72 h,before virus-containing supernatant was collected. Virus wasconcentrated by spinning for 2 h at 24,000 rpm using a SW32Ti rotor.Virus was resuspended overnight at 4 C, allowing pellets to dissolve.Library virus was stored at −80 C prior to use.

Screen

K562 cells were obtained from ATCC and maintained in full DMEM media(10% FBS, Pen/Strep). K562 cells were grown in 1L spinner flasks(Matrical) on magnetic stir plates (Bellco). Cells were always passagedbefore reaching confluency (1e6/ml) and subcultured at a concentrationof 1e5/ml.

Virus Infection

250e6 K562 cells were resuspended to a concentration of 1.5e6 cells/ml.Polybrene (Sigma) was added to 120 ml of the K562 cell suspension at afinal concentration of 4 μg/μl. 2 ml of this cell suspension was placedin each well of 5, 12-well plates. 10 ul of virus was added to each wellfor a target MOI of 0.3, ensuring that most cells incorporated 1 or 0lentivirus particles. Plates were spinfected for 2 h at 1000 g andplaced in an incubator for 1 h, after which media was aspirated. 2 ml offull DMEM media (10% FBS, Pen/Strep) was placed in each well and cellswere resuspended. 12 h later, all wells were pooled into a spinner flaskwith 800 ml of full DMEM media. A sample was taken for virus titrationto ensure that the target MOI was obtained. 24 h after the spinfection,Puromycin (Invitrogen, final concentration of 2 μg/ml) was added tobegin selection for infected cells. Two independent infections wereperformed to control for variability in library infection.

Passaging

Infected cells were passaged before reaching 1e6/ml and maintained inPuromycin-containing conditions for one week after infection. At thispoint, 70e6 cells were pelleted and stored as pre-treatment (Early)samples for each infection replicate.

Experimental Selection

After 1 week of Puromycin selection, cells from each infection replicatewere transferred to experimental conditions of (a) untreated cells, (b)moderate disease and (c) severe disease. 70e6 cells were pelleted andresuspended in media corresponding to each experimental condition. Theuntreated condition was defined as complete DMEM media, (11965-092) with1 mM pyruvate (Invitrogen) added. The moderate disease condition wasdefined as complete DMEM media with 100 nM Antimycin (Sigma) and 1 mMpyruvate. The severe disease condition was defined as 100 nM Antimycin,without pyruvate.

Passaging in Experimental Conditions

Cells were subcultured at 1e5/ml and passaged before reaching 1e6/ml. Ateach passage, 70e6 cells were pelleted and stored for intermediatescreen time points.

Library Prep

Sequencing libraries were prepared as previously described (Shalem etal., Science, 343:84-88 (2014)). Briefly, DNA was extracted using theQiagen Blood and Cell Culture DNA Maxi Kit from 70e6 cells perexperimental condition, for each infection replicate. DNA was thenpurified using Micro Bio-Spin columns (BioRad 732-6224). 25 PCRreactions were performed using Herculase II Fusion DNA Polymerase(Agilent) to amplify the sgRNAs from genomic DNA, at a minimum coverageof 450× per sgRNA. 30 ul from the first pooled PCR samples were used asinput for the second PCR reaction, allowing for attachment of barcodesand sequencing adapters. Barcode replicates were included for themoderate disease condition to ensure that PCR errors were notsubstantially contributing to signal. The final PCR products were run onan agarose gel and the correct size PCR products were gel extracted andsequenced on an Illumina HiSeq 2500 platform at the Broad Institute.

Analysis

Processing of sgRNA Reads

Custom Python and Matlab scripts were written for processing ofsequencing reads. Reads were trimmed to remove barcodes and sequencescorresponding to the GECKO library backbone. A custom bowtie library wascreated for mapping between sgRNA sequences and guide/gene names. Bowtiealignment was performed, allowing for single mismatches. Finally, guideabundance was compiled for each experimental condition and a matrixmapping guide name to abundance for all samples was created.

Identification of Enriched and Depleted SgRNAs

Cell Viability Screen

In order to identify genes which are essential to cell viability, guideabundance was first normalized to total number of reads per sample. Thefold-enrichment was calculated for untreated samples (day 21 afterexperimental selection) relative to pre-treatment conditions (day 1before experimental selection), for both infection replicates. Asinfection replicates were very well correlated (r²>0.8), the top 500most depleted genes (by RIGER analysis; Luo et al., Proc. Natl. Acad.Sci. U.S.A. 105:20380-85 (2008)) were found for each infectionreplicate. The intersect of the 500 most essential genes across bothinfection replicates was determined and crossed with the known list ofmitochondrial proteins, or MitoCarta to identify essential mitochondrialgenes (Pagliarini et al., Cell. 134:112-23 (2008)). RIGER output wasgenerated for each infection replicate (untreated relative topre-treated conditions) and used for Gene Set Enrichment Analysis (GSEA)(Subramanian et al., Proc. Natl. Acad. Sci. U.S.A. 102:15545-50 (2005)).

Enrichment Screen

In order to identify gene knockouts which allow cells to cope withmitochondrial dysfunction, fold-enrichment was calculated for moderateor severe disease conditions relative to pre-treatment conditions. Themost enriched genes were then individually checked for their overalleffect on cell viability (untreated relative to pre-treatmentconditions). Alternatively, fold enrichment was also calculated foruntreated vs. disease conditions. However, this form of analysisconfounds genes which are enriched in disease conditions or selectivelydepleted in untreated conditions. The top hit was found using eitherapproach.

RIGER Analysis

RIGER analysis (Luo et al., 2008) was used to generate a summarystatistic by combining information corresponding to all sgRNAs for agiven gene. SgRNAs were pre-ranked by fold-enrichment between twoconditions. The Kolmogorov-Smirnov method was used with 1000permutations. Gene scores were not adjusted for the number of sgRNAscorresponding to a given gene.

GSEA Analysis

Output from RIGER analysis was used for gene set enrichment analysis(Subramanian et al., 2005). All curated gene sets were used duringanalysis in GseaPreranked mode. All other parameters were set to defaultvalues.

Example 3: Activating the Hypoxia Response

After VHL was confirmed as an effective therapeutic target formitochondrial disease, clinically-relevant options for triggering thehypoxia response were studied. While a VHL-inhibitor has been reported(Buckley et al., J. Am. Chem. Soc. 134:4465-68 (2012)), it is not cellpermeable. However, PHD inhibitors have been extensively developed forthe treatment of anemia of chronic kidney disease and ischemic injury(Rabinowitz, J. Med. Chem. 56:9369-9402 (2013)). The small molecule PHDinhibitor, FG-4592, also known as roxadustat, is currently in Phase IIIclinical trials for chronic kidney disease. FG-4592 shows efficacy intreatment of kidney disease by upregulating the canonical marker of thehypoxia response, erythropoietin (EPO). FG-4592 treatment may mimicVHL-knockout, thus triggering a broader hypoxia transcriptional program.Compounds that trigger the hypoxia response including VHL-inhibitors andPHD inhibitors are therapeutics for mitochondrial dysfunction.Pre-treatment and incubation with FG-4592 almost completely rescued thegrowth defects caused by deficiency of multiple respiratory complexes,in multiple cell lines (FIGS. 12-13). Normal growth rates were minimallyincreased by FG-4592. Complex I, III or V inhibition stunts cell growthin most cell lines, including HT-29s, HEK 293s and K562s. Administering˜50 uM FG-4592 in advance and during respiratory chain dysfunctionnearly or completely rescued this growth defect, in a dose-dependentmanner (FIG. 12-13). Even ATP synthase inhibition, which additionallyaffects membrane potential, was significantly rescued by FG-4592. Thenearly full rescue of the disease state across different cell lines andacross chemical lesions highlights the general utility of this approach.

The rescue mechanism of FG-4592 was characterized by studying its effecton the hypoxia response and energy metabolism. While HIF1α isundetectable during normoxic conditions, treatment with FG-4592stabilized the transcription factor even during normoxia. In hypoxicconditions, FG-4592 stabilized HIF1α beyond the endogenous hypoxiaresponse of untreated cells. It has previously been noted that a paradoxexists between mitochondrial dysfunction and cellular sensing of hypoxia(Chandel et al., Proc. Natl. Acad. Sci. U.S.A. 95:11715-20 (1998)). Incell culture, inhibition of the respiratory chain prevents HIFstabilization, even under low oxygen conditions that would otherwisetrigger the hypoxia response. Proposed explanations include highercellular oxygen tensions and increased ROS production during states ofmitochondrial dysfunction. While this phenomenon has been noted in thehypoxia field, it has received less attention in the context ofmitochondrial disease pathogenesis. If such a paradox extends tomitochondrial disease patients, such individuals may be unable tostabilize HIF in physiological conditions of hypoxia. For example,mitochondrial disease patients may have an aberrant response toischemia, stroke, high altitudes and tumor growth. This paradox wasreplicated in cell culture, demonstrating that respiratory chaininhibition by Antimycin or Oligomycin prevented HIF1α stabilizationduring hypoxia. Of note, FG-4592 treatment bypassed this paradox andenabled HIF1α stabilization in the face of mitochondrial dysfunction,during states of normoxia or hypoxia (FIG. 14). Thus, if this paradoxcontributes to disease pathology in mitochondrial disease patients,FG-4592 may serve as a therapeutic bypass.

The HIF transcriptional response is believed to be protective duringstates of hypoxia, at least in part by causing a rewiring of energymetabolism. By shifting from aerobic respiration to anaerobicglycolysis, the HIF1α response can maintain the energy supply at lowoxygen tensions. FG-4592 caused normoxic stabilization of HIF proteins.Treatment with FG-4592 for 24 h, upregulated transcription of genesinvolved in energy metabolism (FIG. 15). Glycolytic enzymes such ashexokinase 2 (HK2) and glucose transporter 1 (GLUT1) were upregulated inmultiple cell types. Glucose import and phosphorylation arerate-limiting steps in the glycolytic flux of many tissues. Lactatedehydrogenase (LDHA) maintains the redox balance during respiratorychain inhibition and was similarly upregulated with FG-4592 treatment.HIF1α activation is also known to shunt the carbon supply away from theTCA cycle and towards the LDH reaction. Several mechanisms have beenproposed for this shift away from aerobic respiration, includingpyruvate dehydrogenase phosphorylation. In support of this mechanism, asignificant upregulation of pyruvate dehydrogenase kinase (PDK1) wasobserved after FG-4592 treatment. Of note, none of the aforementionedenzymes were upregulated by respiratory chain inhibition alone. Thus,cells were unable to mount the appropriate transcriptional response byendogenous mechanisms. However, FG-4592 treatment triggered the hypoxiatranscriptional program, even during respiratory chain inhibition (FIG.15).

The shift in energy metabolism was confirmed by measuring lactic acid asthe end-product of anaerobic glycolysis and oxygen consumption as aproxy for aerobic respiration. In multiple cell types, anaerobicglycolysis was slightly increased by respiratory chain inhibition,likely as a result of allosteric mechanisms. However, treatment withFG-4592 increased glycolysis by nearly 60% in HT-29 cells, under basalconditions and with respiratory chain inhibition. Thus cells are able toshift towards glycolysis using endogenous defense mechanisms; however, atranscriptional response is needed to increase the glycolytic fluxenough to maintain cellular growth rates. Furthermore, basal oxygenconsumption was decreased with FG-4592 treatment. This may be protectivein the setting of mitochondrial dysfunction, as it may limit the amountof ROS produced by impaired electron transport. Genetic and smallmolecule activation of the HIF pathway enabled cells to cope withmitochondrial dysfunction at multiple steps of the electron transportchain and in multiple cell types. The small molecule, FG-4592,normoxically stabilized HIF and thereby increased glycolysis beyondallosteric mechanisms. Furthermore, it bypassed the paradox betweenmitochondrial dysfunction and HIF stabilization during hypoxia.

Example 4: Zebrafish Model of Mitochondrial Disease

A zebrafish reporter strain was used to monitor activation of thehypoxia transcriptional response (Santhakumar et al., Cancer Res. 72,4017-27 (2012)). The reporter fish has a promoter containing hypoxiaresponse elements (HREs) fused to GFP. Hypoxia exposure or VHL knockdowncauses an increase in GFP expression, allowing for in vivo monitoring ofthe hypoxia response. This model system could be used to monitordrug-target engagement and pharmacodynamics of a HIF activator(Chowdhury et al., ACS Chem Biol. 8:1488-96 (2013)). Furthermore,zebrafish embryos have been shown to have a dose-responsive sensitivityto multiple, specific respiratory chain inhibitors including Antimycin(Pinho et al., Br. J. Pharmacol. 169:1072-90 (2013)).

FG-4592 treatment resulted in a time-dependent increase in fluorescenceof individual reporter fish. After even 6 hours of exposure to 2.5 μMFG-4592, a robust increase in fluorescence was detected (FIG. 16). Thus,FG-4592 engaged the zebrafish prolyl-hydroxylases and triggered thehypoxia transcriptional program. Antimycin inhibits oxygen consumptionof zebrafish embryos (Stackley, et al., PLOS One. 6, e25652 (2011)).Prolonged treatment of Antimycin at low nanomolar concentrationsresulted in death of embryos. Antimycin-induced death of zebrafishembryos was prevented by treating the fish with FG-4592. At intermediateconcentrations of Antimycin, FG-4592 treatment nearly doubled survival(FIG. 17). As both the hypoxia response pathway and mitochondrialfunctions are particularly well conserved, this is expected to berelevant for higher organisms.

Example 5: Hypoxia as a Therapeutic in a Mouse Model of Leigh Syndrome

The genome-wide screen and cellular and zebrafish models identified thehypoxia response as a suppressor of mitochondrial dysfunction. Extendingthese findings to an in vivo model, chronic exposure to moderateenvironmental hypoxia—at 11% O₂, a level known to be tolerated inhumans—was evaluated to determine whether it could alleviate the diseasephenotype in a genetic mouse model of mitochondrial disease.

Leigh syndrome is the most common pediatric form of mitochondrialdisease. Though relatively healthy at birth, patients developirreversible neurodegeneration by two years of age (Lake et al., Journalof Neuropathology & Experimental Neurology. 74(6), 482-492 (2015)).These patients suffer deep, bilaterally symmetric lesions in the graymatter of the brain stem and basal ganglia, with marked gliosis. Mostpatients die between the ages of 3-16 months. To date, over 60 differentgenes have been identified that can underlie this devastating syndrome,with Complex I deficiency being the most frequent biochemical cause ofdisease.

A mouse model of Leigh Syndrome has been generated by disruption of themurine Ndufs4 gene (Kruse et al., Cell metabolism. 7(4), 312-320(2008)). Loss of NDUFS4 in humans leads to one of the more severerecessive forms of Leigh syndrome. The murine model has been studied atatmospheric (21% O₂) levels and faithfully recapitulates much of thereported human disease phenotype. Ndufs4 knockout (KO) mice displayretarded growth rates, have impaired visual acuity, and have a delayedstartle response. Their body temperature falls progressively untilreaching 32° C., shortly before death at 50-60 days of age. Diseasedmice also display locomotor deficits and failure to thrive by 50 days.Their neuro-histopathology closely resembles clinical findings, with asubstantial inflammatory response in the brainstem and cerebellum. Sincethis mouse model is well characterized and representative ofmitochondrial disease progression, chronic hypoxic exposure was testedas a therapeutic strategy in this model.

Ndufs4 KO mice were first studied to determine whether they were able totolerate brief hypoxic exposure and mount a hypoxic response in a mannersimilar to wild type (WT) mice. Three WT mice and three KO mice wereexposed to breathing 8.5% oxygen at sea level pressure for 6 hours. Thisgave the mice sufficient time to mount a transcriptional andtranslational response. Acute exposure of WT mice to hypoxia triggersHIF stabilization, resulting in Epo transcription and translation. After6 hours of exposure, Epo protein levels in plasma were measured andshowed that both WT and KO mice upregulated Epo production to a similarextent, increasing circulating EPO levels by approximately 40-fold.These results demonstrated that KO mice are able to mount a hypoxiatranscriptional response.

Environmental hypoxia of 11% O₂ was generated by adjusting the relativeconcentration of nitrogen and oxygen in the input gas mixture. Thiscreated environmental oxygen tensions similar to those found in the highmountain communities of Nepal and Peru (4,500M) (Pawson et al.,Proceedings of the Royal Society of London B: Biological Sciences194(1114), 83-98 (1976)). A control ambient environment breathing 21% O₂was created with an identical chamber set-up.

Mice were placed in 60 liter plexiglass chambers that were given a gasmixture of compressed air and 100% N₂, compressed air alone, orcompressed air and 100% O₂ (Airgas Inc.). The gas flow rates weremeasured and controlled with rotameters and valves. Oxygenconcentrations were measured several times each day at the outlet of thechambers using an oxygen analyzer (MiniOx I Oxygen Analyzer, OhioMedical Corporation) and the flow rates of air, nitrogen and oxygen weremodified if necessary in order to obtain a stable oxygen concentrationof 11% in the hypoxic chamber (and 55% in the mild-hyperoxia chamber).Soda lime (Sodasorb, Smiths Medical) (approximately 250 g), was placedon the floor of each chamber to scavenge carbon dioxide (CO₂) producedby the animals and replaced every 3 days. The CO₂ concentration in eachchamber as well as the temperature and the humidity were monitoredcontinuously using a dedicated infrared CO₂ analyzer, thermometer andhumidity meter (Extech CO200 Monitor, Extech Instruments). The totalflow of fresh gas flushing each chamber was adjusted between 5 and 10L/min to maintain the chamber CO₂ level below 0.4% and the relativehumidity between 30% and 70%. Mice were exposed to gas treatmentcontinuously for 24 hours per day, 7 days a week.

Ndufs4 KO and control mice were continuously exposed to normoxia orhypoxia (11% O₂) after enrollment in the experiment, excluding temporaryremoval for behavior tests and maintenance three times per week.Untreated Ndufs4 KO mice typically begin to show significant diseaseprogression after approximately 30 days of post-birth air exposure,which is about ten days after weaning. Since hypoxia-related vascularresponses (constriction of pulmonary circulation, dilation of ductusarteriosus) occur in early post-natal development, chronic hypoxicexposure treatments were initiated when mice were 30 days old.

Chronic normobaric hypoxia rescued this model of mitochondrial disease.All normoxia-exposed Ndufs4 KO mice either fulfilled criteria for humaneeuthanasia or died at a median age of approximately 60 days with nonesurviving past 75 days (FIG. 18A). However, there were no deaths inNdufs4 KO mice exposed chronically to breathing 11% O₂ (FIG. 18A).Several mice showed a mild clasping phenotype at ages greater than 120days.

The hypoxia-treated mice showed a striking rescue in all aspects ofhealth that were tested, including body weight gain, core temperaturemaintenance, and neurologic behavior. All Ndufs4 KO mice continued togain weight between 30-37 days of age (FIGS. 18B-C). At this stage,untreated KO mice lost weight, became hypothermic, and died. Incontrast, Ndufs4 KO mice breathing 11% O₂ gained weight for severalweeks, at which point body weight gain slowed, similar to the growthkinetics of WT mice. The growth rate of hypoxia-treated Ndufs4 KO micematched that of hypoxia-treated WT mice, suggesting that the primarycause of weight loss in Ndufs4 KO mice was alleviated by hypoxicexposure. At 30 days of age, untreated Ndufs4 KO mice have similar corebody temperatures to WT mice. By 50 days, there is nearly a 4° C. dropin temperature in the Ndufs4 KO mice (FIG. 18D). However, Ndufs4 KO micetreated with chronic 11% O₂ breathing showed no reduction of core bodytemperature (FIG. 18D). Thus, chronic hypoxic breathing rescues theunderlying metabolic phenotype that directly or indirectly results inalterations of energy and nutrient metabolism.

Ndufs4 KO mice, as well as patients suffering from Leigh syndrome,exhibit striking defects in locomotor activity. Ataxia and failure tothrive are hallmarks of mitochondria dysfunction. Behavioral tests wereperformed in 10 day intervals in normoxia and hypoxia-treated, WT and KOmice. The rotarod test (Caston et al., Neurobiology of learning andmemory, 64:195-202 (1995)) measures the ability of mice to maintain gripstrength, balance, and fatigue resistance on an accelerating, rotatingrod. A rotarod machine (Ugo Basile) was used to measure the ability ofmice to stay on an accelerating, rotating rod. Rotarod parameters wereas follows: acceleration of 5 rpm/m and a maximum speed of 40 rpm. Oneach measurement day, three trials were performed, with individualtrials at least 10 minutes apart to allow mice to recuperate. The mediantime on rotarod is reported. If mice used their body to grasp the rod(rather than walking on it) for more than 10 seconds, this time wasrecorded as time of fall. Age of measurements is +/−5 days for practicalpurposes without any age bias between groups.

At 30 days of age, KO mice breathing air display a slight depression inthe median time they can stay on a rotarod (FIG. 18E). This abilitydeclines by 40 days and at 50 days, untreated KO mice are no longer ableto stay on the rod for more than a few seconds, due to a combination ofmuscular weakness, inability to balance, and loss of visual activity.Hypoxia-treated WT mice performed similarly to normoxia-treated controlmice. Remarkably, KO mice breathing 11% O₂ displayed a near completerescue of this locomotor phenotype.

As a further neurological-behavioral test, spontaneous locomotoractivity was measured as total distance traveled within an hour. Theopen field instrument (Med Associates Inc.) was used to measurespontaneous locomotor activity. Mice were blindly chosen for a given dayand placed in open field chambers for 1 hour. Spontaneous locomotoractivity was measured based on beam breaks and recorded by theinstrument. The traces shown in FIG. 18F are representative of a sick,Ndufs4 KO mouse exposed to 21% O₂ (age of such sickness varies slightlybetween mice), age-matched KO and WT mice exposed to 11% O₂, and WT miceexposed to 21% O₂. Age of measurements is +/−5 days for practicalpurposes without any age bias between groups. Untreated KO mice showdrastically reduced spontaneous locomotor activity (FIG. 18F). Thisdefect was significantly rescued in hypoxia-treated mice, however onlyto 50% of the values of control mice (FIGS. 18F and 20).

Example 6: Modest Hyperoxic Exposure is Lethal for a Murine Model ofLeigh Syndrome

The striking therapeutic effect of hypoxia suggested that oxygen itselfmay be a key molecular parameter determining Leigh disease progression.Thus, the converse environmental scenario of chronic mild hyperoxicexposure was evaluated. WT and Ndufs4 KO mice were exposed to breathing55% normobaric oxygen starting at 30 days of age. No effect on survivalwas observed in WT mice exposed to 55% oxygen. However, all nine Ndufs4KO mice died of severe acute pulmonary edema after 2 to 11 days ofbreathing 55% O₂ (FIG. 18A). On the other hand, Ndufs4 KO mice breathingair die at approximately 3 weeks after starting treatments. The dramaticreduction of survival in 55% O₂ breathing KO mice, along with thedramatic extension of their apparently healthy survival in 11% O₂breathing KO mice, points to the role of arterial oxygen tension indetermining the progression of mitochondrial disease.

Example 7: Clinical Chemistry and Histopathology Following Treatmentwith Hypoxia

Ndufs4 KO mice were further characterized following treatment withchronic hypoxia. Complex 1 Activity was measured in cerebellum tissuefrom mice. Tissue was homogenized in 1 ml of ice-cold PBS using a QiagenTissueLyser II. Approximately 50-100 mg of tissue was used as inputmaterial for the Complex I Enzyme Activity Microplate Assay Kit(ab109721, Abcam). Absorbance was read at 450 nm wavelength and recordedevery 30 seconds for 135 total measurements. Background signal was notsubtracted in data shown.

The circulating blood hematocrit in the KO mice was elevated from 40%during normoxia to approximately 60% during hypoxia, indicating EPOtarget engagement by hypoxic breathing (FIG. 19A). Furthermore, althoughNdufs4 KO mice appear quite healthy following hypoxia treatment, brainComplex I activity remained dramatically reduced to the same levels asuntreated Ndufs4 KO mice (FIG. 19B).

Normoxia-treated KO mice exhibit substantial neuronal degeneration.Lesions are accompanied by Iba-1+ microglial proliferation withinolfactory lobes, cerebellum and brainstem as documented elsewhere(Quintana et al., Proc. Natl. Acad. Sci. U.S.A. 107, 10996-11001(2010)). Mice were anesthetized and the chest cavity was opened and acatheter was placed in the left ventricle. The whole body was perfusedwith ice cold PBS and then with 4% PFA. The brain was dissected out,stored overnight in 4% PFA and then placed in 30% sucrose (in PBS) fortwo days. Formalin-perfused brains were sectioned parasagittally at theolfactory lobes. Two transverse sections of cerebellum and brainstemwere also collected: a rostral section with subjacent pons, and a morecaudal section with medulla oblongata. Immunohistochemistry wasperformed on adjacent tissue sections using an antibody recognizing themicroglial marker Iba-1 (Wako; 2 μg/ml). In contrast to normoxia-treatedKO mice, KO mice breathing 11% O₂ exhibited minimal to no lesions (FIG.19C), and were virtually indistinguishable histologically from WTcontrols.

α-hydroxybutyrate has been identified as a circulating plasma marker ofLeigh syndrome (Legault et al., Cell reports. 13, 981:89 (2015)).Lactate and α-hydroxybutyrate were quantified in mouse plasma by spikingin each corresponding isotope labeled standard (CDN isotope). A seriesof standard solutions of metabolites at seven different concentrationswere prepared in a surrogate matrix buffer (PBS buffer with 30 g/L humanserum albumin). 30 uL of the mouse plasma sample were combined with 20uL of isotope labeled internal standard, vortexed for 10 seconds andspun down for 10 seconds. Metabolite extractions were performed using70% acetonitrile. A Q Exactive Plus Orbitrap Mass Spectrometer coupledto a Dionex UltiMate 3000 UHPLC system (Thermo Fisher Scientific) wasused for LC-MS. The Xbridge amide HILIC column (2.1×100 mm, 2.5 μMparticle size, from Waters 186006091) was used to separate metabolitesand MS was acquired under the negative ionization mode. The column wasmaintained at 27° C. during runs. The mobile phase A was 20 mM ammoniumacetate, 0.25% ammonium hydroxide pH adjusted to 9. The mobile phase Bwas 100% acetonitrile. The MS data acquisition was full scan mode in arange of 70-1000 m/z, with the resolution set at 140,000, the AGC targetat 3E6, and the maximum injection time at 400 msec.

α-hydroxybutyrate was elevated in air-breathing Ndufs4 KO mouse plasma(FIG. 19D). Treatment with chronic hypoxia rescued the elevation of thisdisease marker (FIG. 19D). Similarly, plasma lactate levels wereincreased in Ndufs4 KO mice breathing air between 50-65 days of age,while this was partially rescued by 11% hypoxic exposure (FIG. 19E).Collectively, these laboratory and histopathological studies confirmthat chronic hypoxic exposure to breathing 11% O₂ activates theendogenous hypoxia response. Hypoxia does not fix the proximal lesionwithin mitochondrial Complex I, but rather, prevents the onset ofsubsequent biochemical and histopathological defects.

Example 8: Effects of Treatment with Hypoxia on Disease Pathology

To assess whether hypoxic therapy can reverse establishedneurodegenerative disease, we compared the effects of hypoxia onearly-stage disease and late-stage disease. Ndufs4 mice were chronicallyexposed to hypoxia treatment starting at 30 days of age, termedearly-stage treatment. Alternatively, Ndufs4 mice were chronicallyexposed to hypoxia beginning at 55 days of age, termed late-stagetreatment. Early-stage treatment began prior to the development of anydisease symptoms, allowing for the prevention of disease. Late-stagetreatment began after the disease had already manifested, thus testingfor the reversal of disease.

By 55 days of age, the early-stage hypoxia treatment group weighed 14.2g, due to the ameliorative effects of hypoxia. In contrast, normoxicmice of this age weighed 10.6 g. Chronically exposing these mice tolate-stage hypoxia resulted in an improvement of body weight and bodytemperature trajectory. After one month of hypoxic therapy, the bodyweights of early-stage treatment and late-stage treatment groups wereindistinguishable (FIG. 21A). Core body temperature in normoxic mice was33.5° C. at 55 days of age. Late-stage hypoxic treatment resulted in anincrease of core temperature from 33.5° C. to 35.3° C. within five daysof hypoxia exposure (p<0.05) (FIG. 21B).

Behavior was additionally improved as measured by the ability to stay onan accelerating, rotating rod. By 50 days of age, normoxic KO mice canonly stay on a rotating rod for 35 seconds. Exposing these mice to 50days of late-stage hypoxia treatment partially rescued their ability tostay on the rod from 35 seconds to 82 seconds (FIG. 21C). Furthermore,late-stage hypoxia significantly improved the survival rate of KO mice(FIG. 21D). The median survival age of the rescued cohort was 200+ daysversus 58 days of normoxic controls (HR 9.4 (8.2-65.6) 95CI, p<0.001).

Leigh syndrome patients develop symmetric, bilateral lesions in thebrain. The same mode of pathogenesis has previously been demonstrated innormoxic Ndufs4 KO mice. To determine whether the survival and behaviorrescue effected by late-stage hypoxia treatment are accompanied by areversal of the cerebral lesions, sequential brain MM scans wereperformed in four Ndufs4 KO mice receiving late-stage hypoxia therapy.After the first scan, mice were treated with hypoxia for two weeks and asecond scan was performed (FIG. 22). After four weeks of 11% O₂breathing, a third scan was performed. Neuroimaging demonstrated aprogressive reduction of intensity and size of lesions in the brainstemand olfactory bulbs, which is observable after the first two weeks oftreatment. In late-stage disease mice, the IV ventricle appears morediffuse, likely as a consequence of parenchymal atrophy. This abnormalimaging morphology is reversed upon hypoxia treatment. Theaforementioned disease pattern was reversed in all four mice that werestudied.

The initial cohort of hypoxia-treated mice remained alive at 170 days ofage. Hypoxic exposure was continued to determine the full extent of thesurvival rescue. 50% survival was observed at 270 days of age. Thus,survival duration of hypoxic rescue treatment was nearly 5-fold that ofnormoxic KO mice, however it was not a complete rescue relative towild-type survival. In order to understand the cause of death in thiscohort, we began by studying the neurological status of the old,hypoxia-treated mice to determine whether the original disease hadmanifested.

Immunostaining for the inflammatory marker Iba-1 was performed todetermine whether hypoxia delays death by delaying neuropathology. Boththe cerebellum and olfactory bulb display significant microglialactivation in sick, normoxic KO mice. However, none of thehypoxia-treated mice that were greater than 200 days of age displayedany evidence of neuroinflammation by histopathology (FIG. 23A).T2-weighted MRI imaging was also performed to detect the neurologicallesions. Mice breathing normoxia at 60 days developed lesions in thepostero-lateral portion of the brainstem, localized in the vestibularnuclei (FIG. 23B). These anatomical areas are closely connected to therespiratory center and are responsible for the loss of balance and forovercoming central respiratory failure, typically a terminal event.However, none of the older, hypoxia-treated mice had neurologicallesions that were detectable by MM. Thus, hypoxia appears to reverseneurological lesions as detected by Mill and histopathology, even atgreater than 200 days of age. This suggests that death in old,hypoxia-treated KO mice is likely to be attributable to other organdysfunction (e.g., myocardial failure).

Cardiomyopathy is a common presentation of mitochondrial disease. Theacute nature of death in the old, hypoxia-treated mice suggested thatcardiac dysfunction may play a role in the pathology. A series ofechocardiograms was obtained during air breathing to investigate thecause of death in 250 day-old Ndufs4 KO mice breathing hypoxia. Usinghigh-resolution ultrasound, LV myocardial contractility was studied andfound to be significantly impaired in older, KO mice treated withchronic hypoxia but not in WT controls treated with chronic hypoxia. LVFractional shortening was 37% versus 60% in WT controls (FIG. 24B). Inaddition, echocardiograms were strongly suggestive of chronicpericardial effusions and numerous arrhythmias were noted during thescans. Of note, the right ventricle did not appear hypertrophied.However, measurement of left ventricular internal diameters showedenlarged left ventricular lumens both in systole and diastole (FIG.24C-E). To determine whether such findings are present at an earlierstage in Ndufs4 KO mice breathing 11% oxygen, the same exam wasperformed at 50 days of age (after about 3 weeks of hypoxia exposure).No alteration of LV contractility was detected at this stage (FIG. 24A).This highlights that the pathologic LV cardiac dysfunction observed inold Ndufs4 KO mice breathing hypoxia was not present in the younger micebreathing normoxia. Indeed, it was preceded by lethal neurologicdisease. This suggests that different tissues have altered temporal andoxygen level thresholds for producing oxygen toxicity.

Ndufs4 KO mice were assessed breathing 11% oxygen for ten hours per dayfrom 9 am to 7 pm, and breathing at normoxia for the remaining 14hours/day. Given that mice are nocturnal creatures, in this protocolthey were breathing normoxia while awake and hypoxia while asleep. Thisintermittent exposure to hypoxia increased hematocrit to 55% withinthree weeks, indicative of sufficient physiological adaptation tohypoxia (FIG. 25E). However, survival rates were identical to untreated(normoxic) KO mice (FIG. 25A). During exposure to intermittent hypoxia,body weight decreased until either a natural death or humane euthanasiawas administered. Mice undergoing the intermittent protocol presented at60 days with a lower body weight compared to normoxic KO controls (FIG.25B). Furthermore, body temperature was 32° C. in mice treated withintermittent hypoxia, versus 35° C. of normoxic KO controls (FIG. 25C).The ability of KO mice to remain on an accelerating, rotating rod wastested. No significant improvement was recorded when comparing KO miceexposed to intermittent hypoxia vs. normoxia (FIG. 25D). All MM scans ofNdufs4 KO mice exposed to intermittent hypoxia revealed hyperintenselesions in the brainstem and olfactory bulbs, resembling theneurological lesions of Ndufs4 KO mice breathing normoxia (FIG. 25F).Thus, although this regimen of intermittent hypoxia is sufficient totrigger certain aspects of the hypoxia adaptive program (such ashematocrit elevation), it did not prevent disease progression. In theinitial studies of chronic hypoxia described herein, KO mice werebriefly exposed to normoxia 3-5 times per week to allow for maintenanceof their cages and behavior studies. These mice never developed brainlesions by neuropathology. Thus, some but not all intermittenthypoxia/normoxia regimens are effective.

Hypoxic breathing at 11% oxygen is equivalent to breathing the partialpressure of oxygen found at 4,500 m of altitude. A very mild level ofhypoxia was also assessed, equivalent to 1,500 m of altitude. Breathing17% O₂ did not prevent neurological disease in Ndufs4 KO mice. Theclinical manifestations were similar to Ndufs4 KO mice breathingnormoxic air. A loss in body core temperature was recorded from 36.5° C.to 35.9° C. at 50 days of age (FIG. 26C). Significant weight loss wasalso measured (FIG. 26B). After 3 weeks of chronic 17% oxygen exposure,the tail venous blood hematocrit was 51% (compared to 60% after threeweeks of 11% oxygen exposure) (FIG. 26D). These findings suggest thatthis particular regimen of mild hypoxia is capable of triggering anintermediate physiological response that does not, however, preventneurological disease progression. In this cohort of mice, the mediansurvival time was increased to 70 days, versus 58 days for normoxiccontrols, a slight, but statistically insignificant improvement ofsurvival time (FIG. 26A).

Example 9: Combination Therapy of Hypoxia and Nitric Oxide

High altitudes and chronic hypoxia exposure are known to cause hypoxicpulmonary vasoconstriction (HPV), which ultimately leads to increasedpulmonary arterial pressure and vascular remodeling. Over time, this canresult in right ventricular hypertrophy and affect myocardial function.Nitric oxide has a known vasodilatory effect and has previously beenshown to decrease human HPV. Nitric Oxide is also a knownanti-inflammatory molecule by many pathways and removes superoxide. Miceexposed to breathing a gas mixture of 11% oxygen and low-dose (20-40ppm) nitric oxide survived significantly longer than normoxia treatedmice (FIG. 27A). Mice exposed to hypoxia are able to remain on therotating rod longer than normoxia treated mice (FIG. 27B). Initialresults suggested that diseased mice treated with a gas mixture of 11%oxygen, combined with low-dose nitric oxide perform even better thanjust hypoxia-treated mice.

Example 10: Hypoxia Protects Against LPS-Toxicity in KO Mice

Mitochondrial disease patients are particularly susceptible toinfections. It is believed that that the hyperimmune response ofmitochondrial disease patients may contribute to disease pathogenesis.Furthermore, the mouse model of Leigh Syndrome shows a significantinflammatory response in the brain regions that ultimately suffer fromneurodegeneration and cause death by respiratory failure. Weinvestigated whether the Ndufs4 KO mouse model demonstrated increasedsusceptibility to infection, using LPS as the immune trigger.

A low dose of LPS, which is completely benign to WT mice, was extremelytoxic to Ndufs4 KO mice (FIG. 28A). No deaths were observed in WTanimals within the first few days following LPS injection (5 mg/kg),however a nearly 70% death rate was apparent in Ndufs4 KO mice in thesame time. Of note, LPS injections were given at a young age to WT andKO mice, before the typical disease symptoms are apparent in the Ndufs4KO mice. Thus, the increased sensitivity to LPS is not attributable to aterminal decline in health status.

In order to further understand the mechanism by which hypoxia rescuesdisease symptoms, we investigated whether hypoxia protects against thepathology associated with the hyperimmune response in KO mice. Indeed,acute hypoxic exposure of LPS-treated KO mice improved survival durationnearly 3-fold (FIG. 28A). Body temperature loss upon LPS treatment wasnot significantly rescued by hypoxia treatment, as hypoxia itself causesacute changes in body temperature in both WT and KO mice (FIG. 28B).This finding indicates that the therapeutic effects of hypoxia mayinvolve an ability to suppress the toxic effects of the hyperimmuneresponse in mitochondrial disease mice. As the inflammatory responseinvolves a significant oxidative stress component, this is a primeexample of the therapeutic effect of hypoxia in the setting of anoxidative stress pathology.

OTHER EMBODIMENTS

While the invention has been described in conjunction with the detaileddescription thereof, the foregoing description is intended to illustrateand not limit the scope of the invention, which is defined by the scopeof the appended claims. Other aspects, advantages, and modifications arewithin the scope of the following claims.

1. A method of treating or preventing mitochondrial dysfunction in asubject in need thereof, the method comprising increasing the activityof a hypoxia response in the subject. 2-9. (canceled)
 10. The method ofclaim 1, wherein the method comprises administration of a PHD inhibitor.11-14. (canceled)
 15. A method of treating or preventing mitochondrialdysfunction in a subject in need thereof, the method comprisingadministering to the subject by inhalation a therapeutically effectiveamount of a therapeutic gas comprising between 5 to 20% O₂. 16-36.(canceled)
 37. A method of treating or preventing mitochondrialdysfunction in a subject in need thereof, the method comprising causingthe subject to breathe a therapeutically effective amount of air in ahypobaric chamber. 38-40. (canceled)
 41. The method of claim 15, whereinthe subject has a mitochondrial disorder.
 42. The method of claim 41,wherein the mitochondrial disorder is a monogenic mitochondrialdisorder.
 43. The method of claim 42, wherein the mitochondrial disorderis characterized by a mutation in a gene selected from the groupconsisting of AARS2, AASS, ABAT, ABCB6, ABCB7, ABCD1, ACACA, ACAD8,ACAD9, ACADM, ACADS, ACADSB, ACADVL, ACAT1, ACO2, ACSF3, ACSL4, ADCK3,ADCK4, AFG3L2, AGK, AGXT, AIFM1, AK2, ALAS2, ALDH18A1, ALDH2, ALDH3A2,ALDH4A1, ALDH5A1, ALDH6A1, ALDH7A1, AMACR, AMT, APOPT1, ATIC, ATP5A1,ATPSE, ATP6, ATP8, ATPAF2, ATXN2, AUH, BAX, BCKDHA, BCKDHB, BCKDK,BCS1L, BOLA3, C10orf2, C12orf65, CASA, CARS2, CASP8, CAT, CEP89,CHCHD10, CISD2, CLPB, CLPP, COA5, COA6, COASY, COQ2, COQ4, COQ6, COQ9,COX1, COX10, COX14, COX15, COX2, COX20, COX3, COX4I2, COX6A1, COX6B1,COX7B, CPDX, CPS1, CPT1A, CPT2, CYBSA, CYB5R3, CYC1, CYCS, CYP11A1,CYP11B2, CYP24A1, CYP27A1, CYP27B1, CYTB, D2HGDH, DARS2, DBT, DGUOK,DHCR24, DHODH, DHTKD1, DIABLO, DLAT, DLD, DMGDH, DMPK, DNA2, DNAJC19,DNM1L, EARS2, ECHS1, ELAC2, ETFA, ETFB, ETFDH, ETHE1, FARS2, FASTKD2,FBXL4, FECH, FH, FKBP10, FOXRED1, FXN, GARS, GATM, GCDH, GCSH, GDAP1,GFER, GFM1, GK, GLDC, GLRX5, GLUD1, GLYCTK, GPI, GPX1, GRHPR, GTPBP3,HADH, HADHA, HADHB, HARS2, HCCS, HIBCH, HK1, HMBS, HMGCL, HMGCS2, HOGA1,HSD17B10, HSD17B4, HSPD1, HTRA2, IDH2, IDH3B, ISCA2, ISCU, IVD, KARS,KIF1B, KRT5, L2HGDH, LARS2, LIAS, LONP1, LRPPRC, LYRM4, LYRM7, MAOA,MARS2, MCCC1, MCCC2, MCEE, MFN2, MGME1, MICU1, MLH1, MLYCD, MMAB,MMACHC, MMADHC, MOCS1, MPC1, MPV17, MRPL12, MRPL3, MRPL44, MRPS16,MRPS22, mt-12S rRNA, mt-tRNATyr, mt-tRNATrp, mt-tRNAVal, mt-tRNAThr,mt-tRNASer1, mt-tRNASer2, mt-tRNAArg, mt-tRNAG1n, mt-tRNAPro,mt-tRNAAsn, mt-tRNAMet, mt-tRNALeu1, mt-tRNALeu2, mt-tRNALys,mt-tRNAIle, mt-tRNAHis, mt-tRNAGly, mt-tRNAPhe, mt-tRNAGlu, mt-tRNAAsp,mt-tRNACys, mt-tRNAAla, MTFMT, MTO1, MTPAP, MUT, MUTYH, NAGS, NARS2,NCOA4, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA1, NDUFA10, NDUFA11,NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4,NDUFAF5, NDUFAF6, NDUFB11, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3,NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1, NNT, NUBPL, OAT,OGDH, OGG1, OPA1, OPA3, OTC, OXCT1, PAM16, PANK2, PARK7, PARS2, PC,PCCA, PCCB, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PEX11B,PEX6, PHYH, PINK1, PNPO, PNPT1, POLG, POLG2, PPM1K, PPDX, PRODH, PTRH2,PTS, PUS1, PYCR1, QDPR, RARS, RARS2, RMND1, RPL35A, RPS14, RRM2B, SARS2,SCO1, SCO2, SCP2, SDHA, SDHAF1, SDHAF2, SDHB, SDHC, SDHD, SECISBP2,SERAC1, SFXN4, SLC16A1, SLC19A3, SLC25A1, SLC25A12, SLC25A13, SLC25A15,SLC25A19, SLC25A20, SLC25A22, SLC25A3, SLC25A38, SLC25A4, SNAP29, SOD1,SPG7, SPR, SPTLC2, STAR, SUCLA2, SUCLG1, SUOX, SURF1, TACO1, TARS2, TAZ,TCIRG1, TIMM8A, TK2, TMEM126A, TMEM70, TMLHE, TPI1, TRIT1, TRMU, TRNT1,TSFM, TTC19, TUBB3, TUFM, TYMP, UNG, UQCR10, UQCRB, UQCRC2, UQCRQ,VARS2, WDR81, WFS1, XPNPEP3, and YARS2.
 44. The method of claim 41,wherein the mitochondrial disorder is characterized by a point mutationin the mitochondrial DNA (mtDNA), deletion within the mtDNA, duplicationwithin the mtDNA, or depletion of the mtDNA.
 45. The method of claim 41,wherein the mitochondrial disorder is characterized by a biochemicaldeficiency of respiratory chain Complex I, II, III, IV, V, or acombination thereof.
 46. The method of claim 41, wherein themitochondrial disorder is Kearns-Sayre syndrome (KSS), Leber'shereditary optic neuropathy (LHON), myoclonic epilepsy ragged red fibersyndrome (MERRF), mitochondrial encephalopathy, lactic acidosis, andstroke (MELAS) syndrome, sensory ataxic neuropathy, dysarthria, andophthalmoparesis (SANDO) syndrome, maternally inherited Leigh syndrome(MILS), myopathy and external ophthalmoplegia, neuropathy,gastrointestinal encephalopathy (MNGIE) syndrome, Leigh syndrome,maternally inherited diabetes and deafness (MIDD) syndrome,Alpers-Huttenlocher syndrome, Sengers syndrome, mitochondrial myopathy,lactic acidosis and sideroblastic anemia (MLASA), chronic progressiveexternal ophthalmoplegia (CPEO), autosomal dominant progressive externalophthalmoplegia (AdPEO), neuropathy, ataxia, retinitis pigmentosa (NARP)syndrome, GRACILE syndrome, diabetes insipidus, diabetes mellitus, opticatrophy, and deafness (DIDMOAD) syndrome, or Pearson's syndrome. 47-51.(canceled)
 52. The method of claim 15, wherein the subject has anage-associated disorder.
 53. The method of claim 52, wherein theage-associated disorder is type 2 diabetes, insulin resistance,neurodegeneration, peripheral neuropathy, sarcopenia, muscle atrophy,deafness, atherosclerosis, cardiovascular disease, heart failure,chronic kidney disease, cancer, arthritis, cataracts, or osteoporosis.54-64. (canceled)
 65. A system comprising (i) an enclosed tent orchamber or a breathing apparatus, (ii) a hypoxia induction system thatdelivers oxygen-depleted air to the enclosed tent or chamber or thebreathing apparatus, wherein the oxygen-depleted air comprises between 5to 20% O₂, and (iii) a device that measures arterial oxygen saturationin a subject breathing air within the enclosed tent or chamber or fromthe breathing apparatus, wherein the system adjusts the oxygen contentof the oxygen-depleted air delivered to the enclosed tent or chamber orthe breathing apparatus based upon the oxygen saturation measured by thedevice such that oxygen saturation in the subject is maintained withinthe range of 50% to 90%. 66-72. (canceled)
 73. A method of treating orpreventing an oxidative stress disorder in a subject in need thereof,the method comprising increasing the activity of a hypoxia response inthe subject.
 74. The method of claim 73, wherein the method comprisesadministering to the subject by inhalation a therapeutically effectiveamount of a therapeutic gas comprising between 5 to 20% O₂. 75-96.(canceled)
 97. The method claim 73, wherein the oxidative stressdisorder is Parkinson's disease, Alzheimer's disease, amyotrophiclateral sclerosis, Huntington's disease, multiple sclerosis, Aspergersyndrome, attention deficit hyperactivity disorder, diabetes,cardiovascular disease, cancer, Lafora disease, atherosclerosis, heartfailure, myocardial infarction, fragile X syndrome, sickle cell disease,lichen planus, vitiligo, or autism. 98-102. (canceled)
 103. A method ofscreening for a compound that increases the activity of a hypoxiaresponse comprising a) administering a candidate compound to a first setof one or more cells with a compromised function of the mitochondrialrespiratory chain; b) measuring the growth of the first set of one ormore cells; and c) comparing the growth of the first set of one or morecells to the growth of a second set of one or more cells, wherein thesecond set of one or more cells also have compromised function of themitochondrial respiratory chain, but have not been administered thecandidate compound, wherein if the growth of the first set of cells isgreater than the growth of the second set of cells then the candidatecompound increases the activity of a hypoxia response. 104-114.(canceled)
 115. A composition comprising a nucleic acid moleculecomprising a sequence selected from the group consisting of SEQ IDNOs:1-5, wherein the nucleic acid molecule is functionally integratedwith a viral vector.
 116. A method of treating or preventing aninflammatory disorder in a subject in need thereof, the methodcomprising increasing the activity of a hypoxia response in the subject.117. The method of claim 117, wherein the inflammatory disorder isrheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis,inflammatory bowel disease, psoriasis, inflammatory myositis,Langerhans-cell histiocytosis, adult respiratory distress syndrome,Wegener's granulomatosis, vasculitis, cachexia, stomatitis, idiopathicpulmonary fibrosis, dermatomyositis, polymyositis, non-infectiousscleritis, chronic sarcoidosis with pulmonary involvement,myelodysplastic syndrome, moderate to severe chronic obstructivepulmonary disease without a large right to left shunt, or giant cellarteritis.